Starting phenix.real_space_refine on Mon Mar 25 03:09:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/03_2024/7pqd_13590_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/03_2024/7pqd_13590.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/03_2024/7pqd_13590_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/03_2024/7pqd_13590_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/03_2024/7pqd_13590_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/03_2024/7pqd_13590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/03_2024/7pqd_13590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/03_2024/7pqd_13590_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqd_13590/03_2024/7pqd_13590_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 12 5.49 5 Mg 64 5.21 5 S 202 5.16 5 C 32328 2.51 5 N 6388 2.21 5 O 6956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BD PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bd PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45952 Number of models: 1 Model: "" Number of chains: 144 Chain: "AA" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 394 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AC" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AD" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AE" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AF" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AG" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AH" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AI" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AJ" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AK" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AL" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "AN" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 432 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "BA" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BB" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BC" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "BD" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BE" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BF" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BG" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BH" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BI" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BJ" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "BK" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "BL" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "BM" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "BN" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "H" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1866 Classifications: {'peptide': 246} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Chain: "L" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2444 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "UA" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "UB" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "UU" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 362 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "X" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "aa" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 394 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ab" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ac" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ad" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ae" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "af" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ag" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ah" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ai" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "aj" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "ak" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "al" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "am" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 462 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "an" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 432 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "ba" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bb" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bc" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "bd" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "be" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bf" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bg" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bh" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bi" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bj" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "bk" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "bl" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "bm" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 343 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "bn" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "h" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1866 Classifications: {'peptide': 246} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Chain: "l" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "m" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2444 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 294} Chain: "ua" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "ub" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "uu" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 362 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "x" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "AA" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AB" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SP2': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AC" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 201 Unusual residues: {'3PE': 1, 'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AD" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AF" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AG" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AH" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AI" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AJ" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "AK" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AL" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "AN" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BB" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BD" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BE" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BF" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BG" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BH" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BI" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BJ" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BK" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BL" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BM" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "BN" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 135 Unusual residues: {'3PE': 1, 'CD4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 332 Unusual residues: {'BCL': 2, 'BPH': 1, 'SQD': 1, 'U10': 1, 'UQ1': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "M" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 422 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CD4': 1, 'LMT': 1, 'SP2': 1, 'U10': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "aa" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ab" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SP2': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "ac" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 201 Unusual residues: {'3PE': 1, 'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "ad" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ae" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "af" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SP2': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "ag" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ah" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "ai" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "aj" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SP2': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "ak" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "al" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "am" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "an" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "ba" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bb" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bc" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "bd" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "be" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "bf" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bg" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "bh" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bi" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "bj" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bk" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bl" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SP2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "bm" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "bn" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 135 Unusual residues: {'3PE': 1, 'CD4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 278 Unusual residues: {'BCL': 2, 'BPH': 1, 'U10': 1, 'UQ1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "m" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 422 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CD4': 1, 'LMT': 1, 'SP2': 1, 'U10': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "x" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "BB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "M" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "X" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "ab" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "l" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "m" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "x" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 22.17, per 1000 atoms: 0.48 Number of scatterers: 45952 At special positions: 0 Unit cell: (144.95, 225.55, 106.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 202 16.00 P 12 15.00 Mg 64 11.99 O 6956 8.00 N 6388 7.00 C 32328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=64, symmetry=0 Number of additional bonds: simple=64, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.16 Conformation dependent library (CDL) restraints added in 6.8 seconds 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 8 sheets defined 66.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'AA' and resid 4 through 10 Processing helix chain 'AA' and resid 13 through 36 Processing helix chain 'AA' and resid 39 through 41 No H-bonds generated for 'chain 'AA' and resid 39 through 41' Processing helix chain 'AB' and resid 4 through 10 Processing helix chain 'AB' and resid 13 through 36 removed outlier: 3.659A pdb=" N VALAB 18 " --> pdb=" O ARGAB 14 " (cutoff:3.500A) Processing helix chain 'AB' and resid 43 through 50 Processing helix chain 'AC' and resid 3 through 10 Processing helix chain 'AC' and resid 13 through 36 Processing helix chain 'AC' and resid 43 through 50 Processing helix chain 'AD' and resid 4 through 10 Processing helix chain 'AD' and resid 13 through 36 Processing helix chain 'AD' and resid 43 through 50 Processing helix chain 'AE' and resid 3 through 10 Processing helix chain 'AE' and resid 13 through 37 Processing helix chain 'AE' and resid 43 through 50 removed outlier: 3.529A pdb=" N ALAAE 48 " --> pdb=" O LEUAE 44 " (cutoff:3.500A) Processing helix chain 'AF' and resid 4 through 10 Processing helix chain 'AF' and resid 13 through 37 Processing helix chain 'AF' and resid 43 through 50 Processing helix chain 'AG' and resid 4 through 10 Processing helix chain 'AG' and resid 13 through 37 removed outlier: 3.786A pdb=" N VALAG 18 " --> pdb=" O ARGAG 14 " (cutoff:3.500A) Processing helix chain 'AG' and resid 43 through 50 Processing helix chain 'AH' and resid 4 through 9 Processing helix chain 'AH' and resid 13 through 36 Processing helix chain 'AH' and resid 43 through 50 Processing helix chain 'AI' and resid 4 through 10 Processing helix chain 'AI' and resid 13 through 36 Processing helix chain 'AI' and resid 43 through 50 Processing helix chain 'AJ' and resid 4 through 9 Processing helix chain 'AJ' and resid 13 through 37 Processing helix chain 'AJ' and resid 43 through 50 Processing helix chain 'AK' and resid 3 through 9 Processing helix chain 'AK' and resid 13 through 37 Processing helix chain 'AK' and resid 43 through 50 Processing helix chain 'AL' and resid 4 through 9 Processing helix chain 'AL' and resid 13 through 36 Processing helix chain 'AL' and resid 43 through 50 Processing helix chain 'AM' and resid 3 through 10 Processing helix chain 'AM' and resid 13 through 37 removed outlier: 3.724A pdb=" N ALAAM 19 " --> pdb=" O ARGAM 15 " (cutoff:3.500A) Processing helix chain 'AM' and resid 43 through 50 Processing helix chain 'AN' and resid 5 through 10 Processing helix chain 'AN' and resid 13 through 37 removed outlier: 3.519A pdb=" N VALAN 22 " --> pdb=" O VALAN 18 " (cutoff:3.500A) Processing helix chain 'AN' and resid 43 through 50 removed outlier: 3.810A pdb=" N ALAAN 49 " --> pdb=" O GLUAN 45 " (cutoff:3.500A) Processing helix chain 'BA' and resid 14 through 45 removed outlier: 3.508A pdb=" N SERBA 22 " --> pdb=" O GLNBA 18 " (cutoff:3.500A) Processing helix chain 'BB' and resid 14 through 45 Processing helix chain 'BC' and resid 14 through 45 Processing helix chain 'BD' and resid 14 through 45 Processing helix chain 'BE' and resid 14 through 45 Processing helix chain 'BF' and resid 14 through 45 Processing helix chain 'BG' and resid 14 through 45 Processing helix chain 'BH' and resid 14 through 45 Processing helix chain 'BI' and resid 14 through 45 Processing helix chain 'BJ' and resid 14 through 45 removed outlier: 3.640A pdb=" N SERBJ 22 " --> pdb=" O GLNBJ 18 " (cutoff:3.500A) Processing helix chain 'BK' and resid 14 through 45 Processing helix chain 'BL' and resid 14 through 46 removed outlier: 3.693A pdb=" N SERBL 22 " --> pdb=" O GLNBL 18 " (cutoff:3.500A) Processing helix chain 'BM' and resid 14 through 46 removed outlier: 3.615A pdb=" N TRPBM 45 " --> pdb=" O ALABM 41 " (cutoff:3.500A) Processing helix chain 'BN' and resid 14 through 45 removed outlier: 3.645A pdb=" N VALBN 34 " --> pdb=" O LEUBN 30 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEUBN 40 " --> pdb=" O ILEBN 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 36 Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.783A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 4.090A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.669A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.115A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 225 through 249 removed outlier: 3.891A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 267 Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 37 through 41 removed outlier: 3.562A pdb=" N TRP M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 37 through 41' Processing helix chain 'M' and resid 53 through 77 Processing helix chain 'M' and resid 82 through 87 removed outlier: 3.576A pdb=" N LEU M 86 " --> pdb=" O PRO M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' Processing helix chain 'M' and resid 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 113 through 140 removed outlier: 3.728A pdb=" N ALA M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 161 removed outlier: 3.666A pdb=" N SER M 152 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU M 156 " --> pdb=" O SER M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 removed outlier: 3.772A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 225 Processing helix chain 'M' and resid 227 through 229 No H-bonds generated for 'chain 'M' and resid 227 through 229' Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 removed outlier: 3.532A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 285 removed outlier: 3.887A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 300 Processing helix chain 'UA' and resid 2 through 28 Processing helix chain 'UB' and resid 4 through 27 Processing helix chain 'UU' and resid 6 through 29 removed outlier: 3.832A pdb=" N VALUU 16 " --> pdb=" O METUU 12 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VALUU 19 " --> pdb=" O ALAUU 15 " (cutoff:3.500A) Processing helix chain 'UU' and resid 32 through 47 Processing helix chain 'X' and resid 16 through 54 Processing helix chain 'aa' and resid 4 through 10 Processing helix chain 'aa' and resid 13 through 36 Processing helix chain 'aa' and resid 39 through 41 No H-bonds generated for 'chain 'aa' and resid 39 through 41' Processing helix chain 'ab' and resid 4 through 10 Processing helix chain 'ab' and resid 13 through 36 removed outlier: 3.532A pdb=" N VALab 18 " --> pdb=" O ARGab 14 " (cutoff:3.500A) Processing helix chain 'ab' and resid 43 through 50 Processing helix chain 'ac' and resid 3 through 10 Processing helix chain 'ac' and resid 13 through 36 Processing helix chain 'ac' and resid 43 through 50 Processing helix chain 'ad' and resid 4 through 10 Processing helix chain 'ad' and resid 13 through 36 Processing helix chain 'ad' and resid 43 through 50 Processing helix chain 'ae' and resid 3 through 10 Processing helix chain 'ae' and resid 13 through 37 Processing helix chain 'ae' and resid 43 through 50 removed outlier: 3.530A pdb=" N ALAae 48 " --> pdb=" O LEUae 44 " (cutoff:3.500A) Processing helix chain 'af' and resid 4 through 10 Processing helix chain 'af' and resid 13 through 37 Processing helix chain 'af' and resid 43 through 50 Processing helix chain 'ag' and resid 4 through 10 Processing helix chain 'ag' and resid 13 through 37 removed outlier: 3.799A pdb=" N VALag 18 " --> pdb=" O ARGag 14 " (cutoff:3.500A) Processing helix chain 'ag' and resid 43 through 50 Processing helix chain 'ah' and resid 4 through 9 removed outlier: 3.547A pdb=" N ILEah 7 " --> pdb=" O PHEah 4 " (cutoff:3.500A) Processing helix chain 'ah' and resid 13 through 36 Processing helix chain 'ah' and resid 43 through 50 Processing helix chain 'ai' and resid 4 through 10 Processing helix chain 'ai' and resid 13 through 36 Processing helix chain 'ai' and resid 43 through 50 Processing helix chain 'aj' and resid 4 through 9 Processing helix chain 'aj' and resid 13 through 37 Processing helix chain 'aj' and resid 43 through 50 Processing helix chain 'ak' and resid 3 through 9 Processing helix chain 'ak' and resid 13 through 37 Processing helix chain 'ak' and resid 43 through 50 Processing helix chain 'al' and resid 4 through 9 Processing helix chain 'al' and resid 13 through 36 Processing helix chain 'al' and resid 43 through 50 Processing helix chain 'am' and resid 3 through 10 Processing helix chain 'am' and resid 13 through 37 removed outlier: 3.723A pdb=" N ALAam 19 " --> pdb=" O ARGam 15 " (cutoff:3.500A) Processing helix chain 'am' and resid 43 through 50 Processing helix chain 'an' and resid 5 through 10 Processing helix chain 'an' and resid 13 through 37 removed outlier: 3.519A pdb=" N VALan 22 " --> pdb=" O VALan 18 " (cutoff:3.500A) Processing helix chain 'an' and resid 43 through 50 removed outlier: 3.812A pdb=" N ALAan 49 " --> pdb=" O GLUan 45 " (cutoff:3.500A) Processing helix chain 'ba' and resid 14 through 45 removed outlier: 3.547A pdb=" N SERba 22 " --> pdb=" O GLNba 18 " (cutoff:3.500A) Processing helix chain 'bb' and resid 14 through 45 Processing helix chain 'bc' and resid 14 through 45 Processing helix chain 'bd' and resid 14 through 45 Processing helix chain 'be' and resid 14 through 45 Processing helix chain 'bf' and resid 14 through 45 Processing helix chain 'bg' and resid 14 through 45 Processing helix chain 'bh' and resid 14 through 45 Processing helix chain 'bi' and resid 14 through 45 Processing helix chain 'bj' and resid 14 through 45 removed outlier: 3.640A pdb=" N SERbj 22 " --> pdb=" O GLNbj 18 " (cutoff:3.500A) Processing helix chain 'bk' and resid 14 through 45 Processing helix chain 'bl' and resid 14 through 46 removed outlier: 3.692A pdb=" N SERbl 22 " --> pdb=" O GLNbl 18 " (cutoff:3.500A) Processing helix chain 'bm' and resid 14 through 46 removed outlier: 3.617A pdb=" N TRPbm 45 " --> pdb=" O ALAbm 41 " (cutoff:3.500A) Processing helix chain 'bn' and resid 14 through 45 removed outlier: 3.647A pdb=" N VALbn 34 " --> pdb=" O LEUbn 30 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEUbn 40 " --> pdb=" O ILEbn 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 36 Processing helix chain 'h' and resid 104 through 107 No H-bonds generated for 'chain 'h' and resid 104 through 107' Processing helix chain 'h' and resid 110 through 112 No H-bonds generated for 'chain 'h' and resid 110 through 112' Processing helix chain 'h' and resid 134 through 136 No H-bonds generated for 'chain 'h' and resid 134 through 136' Processing helix chain 'h' and resid 193 through 195 No H-bonds generated for 'chain 'h' and resid 193 through 195' Processing helix chain 'h' and resid 210 through 215 removed outlier: 3.781A pdb=" N PHE h 213 " --> pdb=" O SER h 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA h 214 " --> pdb=" O ASP h 211 " (cutoff:3.500A) Processing helix chain 'h' and resid 227 through 243 removed outlier: 4.092A pdb=" N LEU h 241 " --> pdb=" O VAL h 237 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N MET h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'l' and resid 7 through 9 No H-bonds generated for 'chain 'l' and resid 7 through 9' Processing helix chain 'l' and resid 32 through 56 Processing helix chain 'l' and resid 71 through 73 No H-bonds generated for 'chain 'l' and resid 71 through 73' Processing helix chain 'l' and resid 80 through 82 No H-bonds generated for 'chain 'l' and resid 80 through 82' Processing helix chain 'l' and resid 84 through 111 Processing helix chain 'l' and resid 116 through 132 removed outlier: 3.669A pdb=" N PHE l 123 " --> pdb=" O PHE l 119 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 134 through 139 Processing helix chain 'l' and resid 142 through 144 No H-bonds generated for 'chain 'l' and resid 142 through 144' Processing helix chain 'l' and resid 152 through 164 removed outlier: 4.114A pdb=" N TYR l 164 " --> pdb=" O THR l 160 " (cutoff:3.500A) Processing helix chain 'l' and resid 167 through 169 No H-bonds generated for 'chain 'l' and resid 167 through 169' Processing helix chain 'l' and resid 171 through 198 Processing helix chain 'l' and resid 209 through 220 Processing helix chain 'l' and resid 225 through 249 removed outlier: 3.891A pdb=" N HIS l 230 " --> pdb=" O THR l 226 " (cutoff:3.500A) Processing helix chain 'l' and resid 259 through 267 Processing helix chain 'm' and resid 26 through 28 No H-bonds generated for 'chain 'm' and resid 26 through 28' Processing helix chain 'm' and resid 37 through 41 removed outlier: 3.561A pdb=" N TRP m 41 " --> pdb=" O THR m 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 37 through 41' Processing helix chain 'm' and resid 53 through 77 Processing helix chain 'm' and resid 82 through 87 removed outlier: 3.577A pdb=" N LEU m 86 " --> pdb=" O PRO m 82 " (cutoff:3.500A) Processing helix chain 'm' and resid 99 through 101 No H-bonds generated for 'chain 'm' and resid 99 through 101' Processing helix chain 'm' and resid 109 through 111 No H-bonds generated for 'chain 'm' and resid 109 through 111' Processing helix chain 'm' and resid 113 through 140 removed outlier: 3.731A pdb=" N ALA m 137 " --> pdb=" O THR m 133 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU m 140 " --> pdb=" O ARG m 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 145 through 161 removed outlier: 3.665A pdb=" N SER m 152 " --> pdb=" O TRP m 148 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA m 153 " --> pdb=" O ALA m 149 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU m 156 " --> pdb=" O SER m 152 " (cutoff:3.500A) Processing helix chain 'm' and resid 163 through 168 Processing helix chain 'm' and resid 171 through 173 No H-bonds generated for 'chain 'm' and resid 171 through 173' Processing helix chain 'm' and resid 179 through 192 removed outlier: 3.778A pdb=" N LEU m 183 " --> pdb=" O ILE m 179 " (cutoff:3.500A) Processing helix chain 'm' and resid 196 through 198 No H-bonds generated for 'chain 'm' and resid 196 through 198' Processing helix chain 'm' and resid 200 through 225 Processing helix chain 'm' and resid 227 through 229 No H-bonds generated for 'chain 'm' and resid 227 through 229' Processing helix chain 'm' and resid 234 through 239 Processing helix chain 'm' and resid 243 through 256 removed outlier: 3.531A pdb=" N TRP m 252 " --> pdb=" O ALA m 248 " (cutoff:3.500A) Processing helix chain 'm' and resid 265 through 285 removed outlier: 3.889A pdb=" N VAL m 276 " --> pdb=" O MET m 272 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR m 277 " --> pdb=" O ALA m 273 " (cutoff:3.500A) Processing helix chain 'm' and resid 294 through 300 Processing helix chain 'ua' and resid 2 through 28 Processing helix chain 'ub' and resid 4 through 27 Processing helix chain 'uu' and resid 6 through 29 removed outlier: 3.831A pdb=" N VALuu 16 " --> pdb=" O METuu 12 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VALuu 19 " --> pdb=" O ALAuu 15 " (cutoff:3.500A) Processing helix chain 'uu' and resid 32 through 47 Processing helix chain 'x' and resid 16 through 54 Processing sheet with id= A, first strand: chain 'H' and resid 62 through 65 Processing sheet with id= B, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= C, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.827A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 203 through 205 removed outlier: 3.616A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY H 155 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE H 160 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'h' and resid 62 through 65 Processing sheet with id= F, first strand: chain 'h' and resid 87 through 89 Processing sheet with id= G, first strand: chain 'h' and resid 131 through 133 removed outlier: 6.827A pdb=" N GLU h 180 " --> pdb=" O VAL h 165 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE h 167 " --> pdb=" O PHE h 178 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE h 178 " --> pdb=" O ILE h 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'h' and resid 203 through 205 removed outlier: 3.617A pdb=" N GLY h 162 " --> pdb=" O VAL h 153 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY h 155 " --> pdb=" O ILE h 160 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE h 160 " --> pdb=" O GLY h 155 " (cutoff:3.500A) 2351 hydrogen bonds defined for protein. 6672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.05 Time building geometry restraints manager: 19.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 13109 1.37 - 1.57: 33775 1.57 - 1.78: 88 1.78 - 1.99: 334 1.99 - 2.19: 256 Bond restraints: 47562 Sorted by residual: bond pdb=" C6 SQD L 306 " pdb=" S SQD L 306 " ideal model delta sigma weight residual 1.840 1.614 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C6 SQD x 100 " pdb=" S SQD x 100 " ideal model delta sigma weight residual 1.840 1.615 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" O7 SQD x 100 " pdb=" S SQD x 100 " ideal model delta sigma weight residual 1.509 1.298 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" O7 SQD L 306 " pdb=" S SQD L 306 " ideal model delta sigma weight residual 1.509 1.298 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" O9 SQD x 100 " pdb=" S SQD x 100 " ideal model delta sigma weight residual 1.511 1.304 0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 47557 not shown) Histogram of bond angle deviations from ideal: 84.27 - 99.25: 260 99.25 - 114.23: 27768 114.23 - 129.21: 35851 129.21 - 144.18: 1133 144.18 - 159.16: 196 Bond angle restraints: 65208 Sorted by residual: angle pdb=" C19 SP2AE 101 " pdb=" C18 SP2AE 101 " pdb=" CM6 SP2AE 101 " ideal model delta sigma weight residual 68.23 118.19 -49.96 3.00e+00 1.11e-01 2.77e+02 angle pdb=" C19 SP2ae 102 " pdb=" C18 SP2ae 102 " pdb=" CM6 SP2ae 102 " ideal model delta sigma weight residual 68.23 118.13 -49.90 3.00e+00 1.11e-01 2.77e+02 angle pdb=" C19 SP2AJ 102 " pdb=" C18 SP2AJ 102 " pdb=" CM6 SP2AJ 102 " ideal model delta sigma weight residual 68.23 118.11 -49.88 3.00e+00 1.11e-01 2.76e+02 angle pdb=" C19 SP2AB 102 " pdb=" C18 SP2AB 102 " pdb=" CM6 SP2AB 102 " ideal model delta sigma weight residual 68.23 118.09 -49.86 3.00e+00 1.11e-01 2.76e+02 angle pdb=" C19 SP2am1000 " pdb=" C18 SP2am1000 " pdb=" CM6 SP2am1000 " ideal model delta sigma weight residual 68.23 118.08 -49.85 3.00e+00 1.11e-01 2.76e+02 ... (remaining 65203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 24469 35.94 - 71.88: 852 71.88 - 107.82: 95 107.82 - 143.76: 26 143.76 - 179.70: 18 Dihedral angle restraints: 25460 sinusoidal: 11886 harmonic: 13574 Sorted by residual: dihedral pdb=" C1 BCLac 102 " pdb=" C2 BCLac 102 " pdb=" C3 BCLac 102 " pdb=" C5 BCLac 102 " ideal model delta sinusoidal sigma weight residual 180.00 0.30 179.70 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAC 101 " pdb=" C2 BCLAC 101 " pdb=" C3 BCLAC 101 " pdb=" C5 BCLAC 101 " ideal model delta sinusoidal sigma weight residual 180.00 0.98 179.02 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCLAN 101 " pdb=" C2 BCLAN 101 " pdb=" C3 BCLAN 101 " pdb=" C5 BCLAN 101 " ideal model delta sinusoidal sigma weight residual -180.00 -1.20 -178.80 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 25457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.981: 6384 0.981 - 1.962: 0 1.962 - 2.943: 0 2.943 - 3.924: 0 3.924 - 4.904: 2 Chirality restraints: 6386 Sorted by residual: chirality pdb=" C1 SQD L 306 " pdb=" C2 SQD L 306 " pdb=" O5 SQD L 306 " pdb=" O6 SQD L 306 " both_signs ideal model delta sigma weight residual False -2.39 2.52 -4.90 2.00e-01 2.50e+01 6.01e+02 chirality pdb=" C1 SQD x 100 " pdb=" C2 SQD x 100 " pdb=" O5 SQD x 100 " pdb=" O6 SQD x 100 " both_signs ideal model delta sigma weight residual False -2.39 2.46 -4.85 2.00e-01 2.50e+01 5.89e+02 chirality pdb=" C2C BPH M1003 " pdb=" C1C BPH M1003 " pdb=" C3C BPH M1003 " pdb=" CMC BPH M1003 " both_signs ideal model delta sigma weight residual False -2.81 -2.59 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 6383 not shown) Planarity restraints: 7950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C24 SP2AK 102 " -0.095 2.00e-02 2.50e+03 8.03e-02 8.06e+01 pdb=" C25 SP2AK 102 " 0.125 2.00e-02 2.50e+03 pdb=" C26 SP2AK 102 " 0.042 2.00e-02 2.50e+03 pdb=" C27 SP2AK 102 " -0.077 2.00e-02 2.50e+03 pdb=" CM8 SP2AK 102 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C24 SP2ak 102 " 0.094 2.00e-02 2.50e+03 7.94e-02 7.88e+01 pdb=" C25 SP2ak 102 " -0.123 2.00e-02 2.50e+03 pdb=" C26 SP2ak 102 " -0.041 2.00e-02 2.50e+03 pdb=" C27 SP2ak 102 " 0.076 2.00e-02 2.50e+03 pdb=" CM8 SP2ak 102 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 SP2AA1002 " 0.062 2.00e-02 2.50e+03 6.45e-02 5.20e+01 pdb=" C5 SP2AA1002 " -0.035 2.00e-02 2.50e+03 pdb=" C6 SP2AA1002 " -0.096 2.00e-02 2.50e+03 pdb=" C7 SP2AA1002 " 0.080 2.00e-02 2.50e+03 pdb=" CM3 SP2AA1002 " -0.010 2.00e-02 2.50e+03 ... (remaining 7947 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 284 2.63 - 3.20: 38773 3.20 - 3.77: 74226 3.77 - 4.33: 110370 4.33 - 4.90: 172538 Nonbonded interactions: 396191 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M1006 " model vdw 2.065 2.260 nonbonded pdb=" OE2 GLU m 234 " pdb="FE FE m1008 " model vdw 2.065 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M1006 " model vdw 2.106 2.260 nonbonded pdb=" OE1 GLU m 234 " pdb="FE FE m1008 " model vdw 2.106 2.260 nonbonded pdb=" NE2 HIS l 190 " pdb="FE FE m1008 " model vdw 2.254 2.340 ... (remaining 396186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and resid 4 through 46) selection = (chain 'AD' and resid 4 through 46) selection = (chain 'AL' and resid 4 through 46) selection = (chain 'AN' and resid 4 through 46) selection = (chain 'aa' and resid 4 through 46) selection = (chain 'ag' and resid 4 through 46) selection = (chain 'an' and resid 4 through 46) } ncs_group { reference = (chain 'AB' and resid 1 through 55) selection = (chain 'AC' and resid 1 through 55) selection = (chain 'AE' and resid 1 through 55) selection = (chain 'AF' and resid 1 through 55) selection = (chain 'AG' and resid 1 through 55) selection = (chain 'AH' and resid 1 through 55) selection = (chain 'AI' and resid 1 through 55) selection = (chain 'AJ' and resid 1 through 55) selection = (chain 'AK' and resid 1 through 55) selection = (chain 'AM' and resid 1 through 55) selection = (chain 'ab' and resid 1 through 55) selection = (chain 'ac' and resid 1 through 55) selection = (chain 'ad' and resid 1 through 55) selection = (chain 'ae' and resid 1 through 55) selection = (chain 'af' and resid 1 through 55) selection = (chain 'ah' and resid 1 through 55) selection = (chain 'ai' and resid 1 through 55) selection = (chain 'aj' and resid 1 through 55) selection = (chain 'ak' and resid 1 through 55) selection = (chain 'al' and resid 1 through 55) selection = (chain 'am' and resid 1 through 55) } ncs_group { reference = (chain 'BA' and resid 8 through 49) selection = (chain 'BB' and resid 8 through 49) selection = (chain 'BC' and resid 8 through 49) selection = (chain 'BD' and resid 8 through 49) selection = (chain 'BE' and resid 8 through 49) selection = (chain 'BF' and resid 8 through 49) selection = (chain 'BG' and resid 8 through 49) selection = (chain 'BH' and resid 8 through 49) selection = (chain 'BI' and resid 8 through 49) selection = (chain 'BJ' and resid 8 through 49) selection = (chain 'BK' and resid 8 through 49) selection = (chain 'BL' and resid 8 through 49) selection = (chain 'BM' and resid 8 through 49) selection = (chain 'ba' and resid 8 through 49) selection = (chain 'bb' and resid 8 through 49) selection = (chain 'bc' and resid 8 through 49) selection = (chain 'bd' and resid 8 through 49) selection = (chain 'be' and resid 8 through 49) selection = (chain 'bf' and resid 8 through 49) selection = (chain 'bg' and resid 8 through 49) selection = (chain 'bh' and resid 8 through 49) selection = (chain 'bi' and resid 8 through 49) selection = (chain 'bj' and resid 8 through 49) selection = (chain 'bk' and resid 8 through 49) selection = (chain 'bl' and resid 8 through 49) selection = (chain 'bm' and resid 8 through 49) } ncs_group { reference = chain 'BN' selection = chain 'bn' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = (chain 'L' and (resid 1 through 281 or resid 301 or resid 303)) selection = (chain 'l' and (resid 1 through 281 or resid 301 or resid 303)) } ncs_group { reference = (chain 'M' and (resid 1 through 307 or resid 1001)) selection = (chain 'm' and (resid 1 through 307 or resid 1001)) } ncs_group { reference = chain 'UA' selection = chain 'UB' selection = chain 'ua' selection = chain 'ub' } ncs_group { reference = chain 'UU' selection = chain 'uu' } ncs_group { reference = chain 'X' selection = (chain 'x' and resid 15 through 69) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 32.020 Check model and map are aligned: 0.670 Set scattering table: 0.360 Process input model: 109.340 Find NCS groups from input model: 3.570 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.226 47562 Z= 0.830 Angle : 4.900 49.964 65208 Z= 1.659 Chirality : 0.097 4.904 6386 Planarity : 0.009 0.121 7950 Dihedral : 18.655 179.702 16736 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.18 % Favored : 97.73 % Rotamer: Outliers : 0.36 % Allowed : 1.69 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.11), residues: 4532 helix: -0.34 (0.08), residues: 3198 sheet: 0.11 (0.66), residues: 44 loop : -0.05 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 265 HIS 0.011 0.002 HIS l 153 PHE 0.027 0.002 PHEBA 49 TYR 0.033 0.005 TYRbl 9 ARG 0.025 0.003 ARGbm 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 843 time to evaluate : 4.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 3 LYS cc_start: 0.7358 (mttt) cc_final: 0.7078 (mptt) REVERT: AA 6 LYS cc_start: 0.8168 (mttt) cc_final: 0.7926 (mtpp) REVERT: AC 30 MET cc_start: 0.8250 (ttt) cc_final: 0.8038 (ttm) REVERT: AD 52 ASN cc_start: 0.7422 (m110) cc_final: 0.7046 (m110) REVERT: AH 9 MET cc_start: 0.6356 (mtm) cc_final: 0.5959 (mtm) REVERT: AI 9 MET cc_start: 0.6961 (mtp) cc_final: 0.6733 (mtp) REVERT: AJ 20 GLN cc_start: 0.7686 (tt0) cc_final: 0.7335 (tt0) REVERT: AK 11 PHE cc_start: 0.6391 (m-80) cc_final: 0.6125 (m-10) REVERT: AL 41 TYR cc_start: 0.6841 (m-80) cc_final: 0.6367 (m-80) REVERT: AM 14 ARG cc_start: 0.5150 (mtm180) cc_final: 0.4654 (mtm-85) REVERT: BB 19 GLU cc_start: 0.7707 (tp30) cc_final: 0.7392 (tp30) REVERT: BC 14 ASP cc_start: 0.7716 (t70) cc_final: 0.7329 (t70) REVERT: BD 9 TYR cc_start: 0.8017 (m-80) cc_final: 0.7801 (m-80) REVERT: BN 25 MET cc_start: 0.5192 (tpp) cc_final: 0.4832 (mmm) REVERT: H 52 ASN cc_start: 0.7950 (p0) cc_final: 0.7411 (t0) REVERT: H 70 ARG cc_start: 0.8298 (mtt180) cc_final: 0.8052 (mtt180) REVERT: H 184 LYS cc_start: 0.6847 (mmtt) cc_final: 0.6135 (mtpt) REVERT: H 209 SER cc_start: 0.8073 (p) cc_final: 0.7779 (p) REVERT: H 212 LEU cc_start: 0.7985 (mt) cc_final: 0.7715 (mt) REVERT: H 231 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7756 (t70) REVERT: L 202 LYS cc_start: 0.7570 (mmtt) cc_final: 0.7350 (mmmm) REVERT: M 2 GLU cc_start: 0.5756 (pt0) cc_final: 0.5338 (mm-30) REVERT: M 20 MET cc_start: 0.8323 (mmm) cc_final: 0.8000 (mmp) REVERT: M 22 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7919 (mm-30) REVERT: M 23 ASP cc_start: 0.7389 (m-30) cc_final: 0.6889 (m-30) REVERT: M 26 LEU cc_start: 0.7771 (mt) cc_final: 0.7453 (tp) REVERT: M 61 PHE cc_start: 0.7420 (t80) cc_final: 0.6285 (m-10) REVERT: M 86 LEU cc_start: 0.8673 (tp) cc_final: 0.8322 (mt) REVERT: M 216 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.7936 (t80) REVERT: UA 1 MET cc_start: 0.2481 (ttt) cc_final: 0.1866 (mtp) REVERT: UB 1 MET cc_start: 0.4629 (ttt) cc_final: 0.4130 (mtp) REVERT: aa 3 LYS cc_start: 0.7613 (mttt) cc_final: 0.7393 (mptt) REVERT: ac 3 LYS cc_start: 0.7304 (mttt) cc_final: 0.7032 (mtmt) REVERT: ac 30 MET cc_start: 0.8097 (ttt) cc_final: 0.7804 (ttm) REVERT: ad 9 MET cc_start: 0.7956 (mpp) cc_final: 0.7747 (mpt) REVERT: ad 52 ASN cc_start: 0.7411 (m110) cc_final: 0.6995 (m110) REVERT: ah 9 MET cc_start: 0.6350 (mtm) cc_final: 0.5957 (mtm) REVERT: ai 9 MET cc_start: 0.6941 (mtp) cc_final: 0.6690 (mtm) REVERT: aj 9 MET cc_start: 0.6478 (mtt) cc_final: 0.6147 (mmm) REVERT: aj 20 GLN cc_start: 0.7777 (tt0) cc_final: 0.7369 (tt0) REVERT: ak 11 PHE cc_start: 0.6401 (m-80) cc_final: 0.6158 (m-10) REVERT: al 41 TYR cc_start: 0.6961 (m-80) cc_final: 0.6488 (m-80) REVERT: am 14 ARG cc_start: 0.5156 (mtm180) cc_final: 0.4654 (mtm-85) REVERT: bb 19 GLU cc_start: 0.7719 (tp30) cc_final: 0.7423 (tp30) REVERT: bc 14 ASP cc_start: 0.7765 (t70) cc_final: 0.7447 (t70) REVERT: bd 9 TYR cc_start: 0.8018 (m-80) cc_final: 0.7801 (m-80) REVERT: bn 25 MET cc_start: 0.5426 (tpp) cc_final: 0.5151 (mmm) REVERT: h 52 ASN cc_start: 0.7940 (p0) cc_final: 0.7399 (t0) REVERT: h 70 ARG cc_start: 0.8282 (mtt180) cc_final: 0.8046 (mtt180) REVERT: h 184 LYS cc_start: 0.6871 (mmtt) cc_final: 0.6119 (mtpt) REVERT: h 209 SER cc_start: 0.8124 (p) cc_final: 0.7855 (p) REVERT: h 231 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7758 (t70) REVERT: l 202 LYS cc_start: 0.7568 (mmtt) cc_final: 0.7353 (mmmm) REVERT: m 2 GLU cc_start: 0.5754 (pt0) cc_final: 0.5320 (mm-30) REVERT: m 20 MET cc_start: 0.8317 (mmm) cc_final: 0.7980 (mmp) REVERT: m 22 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7918 (mm-30) REVERT: m 23 ASP cc_start: 0.7395 (m-30) cc_final: 0.6889 (m-30) REVERT: m 26 LEU cc_start: 0.7757 (mt) cc_final: 0.7446 (tp) REVERT: m 61 PHE cc_start: 0.7478 (t80) cc_final: 0.6324 (m-10) REVERT: m 86 LEU cc_start: 0.8664 (tp) cc_final: 0.8312 (mt) REVERT: m 216 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.7936 (t80) REVERT: ua 1 MET cc_start: 0.2486 (ttt) cc_final: 0.1807 (mtp) REVERT: ub 1 MET cc_start: 0.4609 (ttt) cc_final: 0.4125 (mtp) outliers start: 14 outliers final: 2 residues processed: 853 average time/residue: 1.3596 time to fit residues: 1471.7953 Evaluate side-chains 685 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 679 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 216 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 1.9990 chunk 335 optimal weight: 5.9990 chunk 185 optimal weight: 0.2980 chunk 114 optimal weight: 5.9990 chunk 225 optimal weight: 0.7980 chunk 178 optimal weight: 0.2980 chunk 346 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 20 GLN AB 20 GLN AE 20 GLN AF 52 ASN ** AJ 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 42 ASN BK 21 HIS H 147 ASN M 188 ASN M 293 ASN X 58 GLN aa 20 GLN ** ab 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ae 20 GLN af 52 ASN ** ag 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** aj 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ak 42 ASN bd 16 GLN h 147 ASN l 183 ASN m 188 ASN m 293 ASN x 58 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 47562 Z= 0.201 Angle : 2.591 32.383 65208 Z= 0.880 Chirality : 0.038 0.202 6386 Planarity : 0.004 0.036 7950 Dihedral : 19.760 179.954 8638 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.29 % Allowed : 7.38 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.12), residues: 4532 helix: 2.06 (0.09), residues: 3102 sheet: 0.87 (0.71), residues: 44 loop : 0.60 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPAM 8 HIS 0.010 0.001 HIS l 153 PHE 0.023 0.001 PHE M 68 TYR 0.015 0.001 TYRbi 24 ARG 0.004 0.000 ARGAL 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 724 time to evaluate : 4.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AA 3 LYS cc_start: 0.7403 (mttt) cc_final: 0.6976 (mptt) REVERT: AB 9 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.8075 (mtp) REVERT: AB 20 GLN cc_start: 0.8323 (tt0) cc_final: 0.8040 (tt0) REVERT: AC 9 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7024 (mpt) REVERT: AC 12 ASP cc_start: 0.8083 (t0) cc_final: 0.7700 (t0) REVERT: AC 30 MET cc_start: 0.8331 (ttt) cc_final: 0.8092 (ttm) REVERT: AD 52 ASN cc_start: 0.7537 (m110) cc_final: 0.7098 (m110) REVERT: AE 17 PHE cc_start: 0.7850 (m-10) cc_final: 0.7593 (m-80) REVERT: AF 8 TRP cc_start: 0.7832 (m100) cc_final: 0.7609 (m100) REVERT: AG 8 TRP cc_start: 0.7481 (m100) cc_final: 0.7132 (m100) REVERT: AG 36 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8692 (mt) REVERT: AH 9 MET cc_start: 0.6456 (mtm) cc_final: 0.6192 (mtt) REVERT: AI 9 MET cc_start: 0.6939 (mtp) cc_final: 0.6426 (mtt) REVERT: AI 20 GLN cc_start: 0.7509 (tt0) cc_final: 0.7292 (pt0) REVERT: AJ 20 GLN cc_start: 0.7502 (tt0) cc_final: 0.7223 (tt0) REVERT: AK 11 PHE cc_start: 0.6481 (m-80) cc_final: 0.6225 (m-10) REVERT: AL 41 TYR cc_start: 0.6647 (m-80) cc_final: 0.6254 (m-80) REVERT: AM 14 ARG cc_start: 0.4904 (mtm180) cc_final: 0.4431 (mtm180) REVERT: BA 15 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: BD 9 TYR cc_start: 0.7916 (m-80) cc_final: 0.7704 (m-80) REVERT: BD 30 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8200 (tm) REVERT: BG 30 LEU cc_start: 0.8052 (tp) cc_final: 0.7795 (tp) REVERT: BH 12 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6761 (mp) REVERT: BK 23 VAL cc_start: 0.6845 (t) cc_final: 0.6588 (m) REVERT: BM 25 MET cc_start: 0.5946 (mmt) cc_final: 0.5629 (mmm) REVERT: BN 25 MET cc_start: 0.5115 (tpp) cc_final: 0.4679 (mmm) REVERT: H 52 ASN cc_start: 0.7924 (p0) cc_final: 0.7338 (t0) REVERT: H 82 ASP cc_start: 0.5590 (m-30) cc_final: 0.4677 (t0) REVERT: H 209 SER cc_start: 0.7939 (p) cc_final: 0.7682 (p) REVERT: H 212 LEU cc_start: 0.8118 (mt) cc_final: 0.7884 (mt) REVERT: L 202 LYS cc_start: 0.7534 (mmtt) cc_final: 0.7315 (mmmm) REVERT: M 20 MET cc_start: 0.8289 (mmm) cc_final: 0.7997 (mmp) REVERT: M 22 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7948 (mm-30) REVERT: M 26 LEU cc_start: 0.7665 (mt) cc_final: 0.7396 (tp) REVERT: M 61 PHE cc_start: 0.7177 (t80) cc_final: 0.6249 (m-10) REVERT: M 86 LEU cc_start: 0.8664 (tp) cc_final: 0.8373 (mt) REVERT: UA 1 MET cc_start: 0.2378 (ttt) cc_final: 0.1686 (mtp) REVERT: aa 3 LYS cc_start: 0.7668 (mttt) cc_final: 0.7226 (mttp) REVERT: ab 9 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7977 (mtp) REVERT: ac 3 LYS cc_start: 0.7230 (mttt) cc_final: 0.6981 (mtmt) REVERT: ac 12 ASP cc_start: 0.8011 (t0) cc_final: 0.7656 (t0) REVERT: ac 30 MET cc_start: 0.8169 (ttt) cc_final: 0.7927 (ttm) REVERT: ad 9 MET cc_start: 0.7961 (mpp) cc_final: 0.7726 (mpt) REVERT: ad 52 ASN cc_start: 0.7489 (m110) cc_final: 0.7032 (m110) REVERT: ae 17 PHE cc_start: 0.7799 (m-10) cc_final: 0.7542 (m-80) REVERT: af 8 TRP cc_start: 0.7803 (m100) cc_final: 0.7573 (m100) REVERT: ah 9 MET cc_start: 0.6398 (mtm) cc_final: 0.6137 (mtt) REVERT: ai 9 MET cc_start: 0.6933 (mtp) cc_final: 0.6504 (mtm) REVERT: aj 9 MET cc_start: 0.6404 (mtt) cc_final: 0.6197 (mpt) REVERT: aj 20 GLN cc_start: 0.7603 (tt0) cc_final: 0.7303 (tt0) REVERT: ak 11 PHE cc_start: 0.6499 (m-80) cc_final: 0.6271 (m-10) REVERT: al 41 TYR cc_start: 0.6665 (m-80) cc_final: 0.6315 (m-80) REVERT: am 14 ARG cc_start: 0.4864 (mtm180) cc_final: 0.4409 (mtm180) REVERT: bg 30 LEU cc_start: 0.8075 (tp) cc_final: 0.7825 (tp) REVERT: bh 12 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6696 (mp) REVERT: bm 25 MET cc_start: 0.6023 (mmt) cc_final: 0.5703 (mmm) REVERT: bn 25 MET cc_start: 0.5397 (tpp) cc_final: 0.5035 (mmm) REVERT: h 52 ASN cc_start: 0.7916 (p0) cc_final: 0.7309 (t0) REVERT: h 82 ASP cc_start: 0.5604 (m-30) cc_final: 0.4685 (t0) REVERT: h 163 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7469 (pttp) REVERT: l 202 LYS cc_start: 0.7534 (mmtt) cc_final: 0.7321 (mmmm) REVERT: m 20 MET cc_start: 0.8302 (mmm) cc_final: 0.8002 (mmp) REVERT: m 22 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7925 (mm-30) REVERT: m 26 LEU cc_start: 0.7661 (mt) cc_final: 0.7403 (tp) REVERT: m 61 PHE cc_start: 0.7233 (t80) cc_final: 0.6272 (m-10) REVERT: m 86 LEU cc_start: 0.8663 (tp) cc_final: 0.8363 (mt) REVERT: ua 1 MET cc_start: 0.2404 (ttt) cc_final: 0.1718 (mtp) outliers start: 88 outliers final: 25 residues processed: 761 average time/residue: 1.2965 time to fit residues: 1263.6987 Evaluate side-chains 702 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 668 time to evaluate : 4.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 9 MET Chi-restraints excluded: chain AC residue 9 MET Chi-restraints excluded: chain AE residue 5 TYR Chi-restraints excluded: chain AF residue 10 ILE Chi-restraints excluded: chain AG residue 36 LEU Chi-restraints excluded: chain AN residue 30 MET Chi-restraints excluded: chain BA residue 15 GLU Chi-restraints excluded: chain BA residue 26 SER Chi-restraints excluded: chain BD residue 30 LEU Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BH residue 10 THR Chi-restraints excluded: chain BH residue 12 LEU Chi-restraints excluded: chain BI residue 22 SER Chi-restraints excluded: chain BJ residue 44 ILE Chi-restraints excluded: chain BK residue 25 MET Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain UA residue 22 MET Chi-restraints excluded: chain ab residue 9 MET Chi-restraints excluded: chain ae residue 5 TYR Chi-restraints excluded: chain af residue 10 ILE Chi-restraints excluded: chain af residue 14 ARG Chi-restraints excluded: chain an residue 30 MET Chi-restraints excluded: chain ba residue 15 GLU Chi-restraints excluded: chain ba residue 26 SER Chi-restraints excluded: chain bd residue 40 LEU Chi-restraints excluded: chain bg residue 23 VAL Chi-restraints excluded: chain bh residue 12 LEU Chi-restraints excluded: chain bi residue 22 SER Chi-restraints excluded: chain bj residue 44 ILE Chi-restraints excluded: chain bk residue 25 MET Chi-restraints excluded: chain bl residue 40 LEU Chi-restraints excluded: chain h residue 163 LYS Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain ua residue 22 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 334 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 402 optimal weight: 7.9990 chunk 434 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 398 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 322 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 20 GLN AD 20 GLN AE 20 GLN ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS H 32 GLN L 60 ASN M 188 ASN X 58 GLN ab 20 GLN ac 20 GLN ad 20 GLN ae 20 GLN ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** aj 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS l 60 ASN m 188 ASN x 58 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 47562 Z= 0.474 Angle : 2.628 31.012 65208 Z= 0.902 Chirality : 0.049 0.264 6386 Planarity : 0.006 0.043 7950 Dihedral : 20.365 179.992 8630 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.43 % Allowed : 9.52 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.12), residues: 4532 helix: 1.32 (0.09), residues: 3144 sheet: 0.55 (0.68), residues: 44 loop : -0.06 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP m 157 HIS 0.016 0.003 HIS L 153 PHE 0.025 0.003 PHEaa 25 TYR 0.028 0.003 TYRAL 41 ARG 0.006 0.001 ARGbf 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 653 time to evaluate : 4.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: AA 3 LYS cc_start: 0.7697 (mttt) cc_final: 0.7006 (mptt) REVERT: AC 10 ILE cc_start: 0.8060 (mm) cc_final: 0.7789 (mt) REVERT: AC 15 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6382 (mtp-110) REVERT: AC 30 MET cc_start: 0.8375 (ttt) cc_final: 0.8101 (ttm) REVERT: AD 52 ASN cc_start: 0.7559 (m110) cc_final: 0.7131 (m110) REVERT: AE 7 ILE cc_start: 0.7801 (tp) cc_final: 0.7350 (OUTLIER) REVERT: AG 36 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8787 (mt) REVERT: AH 9 MET cc_start: 0.6494 (mtm) cc_final: 0.6288 (mtt) REVERT: AI 9 MET cc_start: 0.6889 (mtp) cc_final: 0.6668 (mtp) REVERT: AI 20 GLN cc_start: 0.7689 (tt0) cc_final: 0.7421 (pt0) REVERT: AJ 20 GLN cc_start: 0.7632 (tt0) cc_final: 0.7328 (tt0) REVERT: AJ 45 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: AK 11 PHE cc_start: 0.6565 (m-80) cc_final: 0.6332 (m-10) REVERT: AM 14 ARG cc_start: 0.5213 (mtm180) cc_final: 0.4725 (mtm180) REVERT: BB 19 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: BD 10 THR cc_start: 0.8213 (p) cc_final: 0.7794 (m) REVERT: BD 30 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8304 (tm) REVERT: BF 14 ASP cc_start: 0.6120 (t0) cc_final: 0.5842 (m-30) REVERT: BG 30 LEU cc_start: 0.8088 (tp) cc_final: 0.7795 (tp) REVERT: BH 40 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8350 (tt) REVERT: BN 25 MET cc_start: 0.5242 (tpp) cc_final: 0.4731 (mmm) REVERT: H 52 ASN cc_start: 0.7872 (p0) cc_final: 0.7278 (t0) REVERT: H 82 ASP cc_start: 0.5708 (m-30) cc_final: 0.4698 (t0) REVERT: H 184 LYS cc_start: 0.6972 (mmtt) cc_final: 0.6153 (mtmt) REVERT: L 202 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7333 (mmmm) REVERT: M 2 GLU cc_start: 0.6241 (pt0) cc_final: 0.6015 (pt0) REVERT: M 20 MET cc_start: 0.8262 (mmm) cc_final: 0.7992 (mmp) REVERT: M 26 LEU cc_start: 0.7816 (mt) cc_final: 0.7597 (tp) REVERT: M 86 LEU cc_start: 0.8712 (tp) cc_final: 0.8417 (mt) REVERT: M 216 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.7968 (t80) REVERT: UA 1 MET cc_start: 0.2827 (ttt) cc_final: 0.2041 (mtp) REVERT: UB 8 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6358 (mp) REVERT: UU 6 GLU cc_start: 0.4812 (OUTLIER) cc_final: 0.4359 (mt-10) REVERT: aa 3 LYS cc_start: 0.7799 (mttt) cc_final: 0.7365 (mttp) REVERT: ac 3 LYS cc_start: 0.7459 (mttt) cc_final: 0.7082 (mtmt) REVERT: ac 9 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.6664 (mpt) REVERT: ac 10 ILE cc_start: 0.8154 (mm) cc_final: 0.7868 (mt) REVERT: ac 15 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6428 (mtp-110) REVERT: ac 30 MET cc_start: 0.8239 (ttt) cc_final: 0.7945 (ttm) REVERT: ad 52 ASN cc_start: 0.7528 (m110) cc_final: 0.7099 (m110) REVERT: ae 7 ILE cc_start: 0.7745 (tp) cc_final: 0.7203 (pt) REVERT: af 14 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.6432 (mtp-110) REVERT: ag 36 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8803 (mt) REVERT: ah 9 MET cc_start: 0.6441 (mtm) cc_final: 0.6214 (mtt) REVERT: ai 9 MET cc_start: 0.6865 (mtp) cc_final: 0.6614 (mtp) REVERT: aj 20 GLN cc_start: 0.7755 (tt0) cc_final: 0.7386 (tt0) REVERT: aj 45 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: ak 11 PHE cc_start: 0.6648 (m-80) cc_final: 0.6442 (m-10) REVERT: al 50 LYS cc_start: 0.6375 (ttmt) cc_final: 0.6082 (ttmm) REVERT: am 14 ARG cc_start: 0.5205 (mtm180) cc_final: 0.4682 (mtm180) REVERT: bb 19 GLU cc_start: 0.7570 (tp30) cc_final: 0.7362 (tp30) REVERT: bd 10 THR cc_start: 0.8234 (p) cc_final: 0.7777 (m) REVERT: bd 26 SER cc_start: 0.7977 (OUTLIER) cc_final: 0.7624 (t) REVERT: bf 14 ASP cc_start: 0.6103 (t0) cc_final: 0.5833 (m-30) REVERT: bg 30 LEU cc_start: 0.8101 (tp) cc_final: 0.7814 (tp) REVERT: bh 40 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8389 (tt) REVERT: bn 25 MET cc_start: 0.5539 (tpp) cc_final: 0.5114 (mmm) REVERT: h 52 ASN cc_start: 0.7852 (p0) cc_final: 0.7265 (t0) REVERT: h 82 ASP cc_start: 0.5695 (m-30) cc_final: 0.4685 (t0) REVERT: h 163 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7473 (pttp) REVERT: h 184 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6094 (mtmt) REVERT: l 202 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7343 (mmmm) REVERT: m 20 MET cc_start: 0.8257 (mmm) cc_final: 0.7984 (mmp) REVERT: m 26 LEU cc_start: 0.7812 (mt) cc_final: 0.7583 (tp) REVERT: m 72 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7918 (tt) REVERT: m 86 LEU cc_start: 0.8708 (tp) cc_final: 0.8408 (mt) REVERT: m 216 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.7962 (t80) REVERT: ua 1 MET cc_start: 0.2768 (ttt) cc_final: 0.2036 (mtp) REVERT: ub 8 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.6341 (mp) REVERT: uu 6 GLU cc_start: 0.4900 (OUTLIER) cc_final: 0.4521 (mt-10) REVERT: x 42 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7937 (mt) outliers start: 132 outliers final: 49 residues processed: 710 average time/residue: 1.3445 time to fit residues: 1214.8599 Evaluate side-chains 687 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 617 time to evaluate : 4.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 15 ARG Chi-restraints excluded: chain AE residue 5 TYR Chi-restraints excluded: chain AF residue 10 ILE Chi-restraints excluded: chain AF residue 14 ARG Chi-restraints excluded: chain AG residue 36 LEU Chi-restraints excluded: chain AJ residue 33 LEU Chi-restraints excluded: chain AJ residue 37 SER Chi-restraints excluded: chain AJ residue 45 GLU Chi-restraints excluded: chain AL residue 10 ILE Chi-restraints excluded: chain AL residue 29 VAL Chi-restraints excluded: chain BA residue 15 GLU Chi-restraints excluded: chain BA residue 26 SER Chi-restraints excluded: chain BB residue 19 GLU Chi-restraints excluded: chain BD residue 30 LEU Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BF residue 26 SER Chi-restraints excluded: chain BH residue 40 LEU Chi-restraints excluded: chain BI residue 22 SER Chi-restraints excluded: chain BI residue 36 ILE Chi-restraints excluded: chain BJ residue 44 ILE Chi-restraints excluded: chain BK residue 25 MET Chi-restraints excluded: chain BK residue 36 ILE Chi-restraints excluded: chain BL residue 40 LEU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 82 LYS Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain UB residue 8 ILE Chi-restraints excluded: chain UU residue 6 GLU Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain ac residue 9 MET Chi-restraints excluded: chain ac residue 15 ARG Chi-restraints excluded: chain ad residue 47 SER Chi-restraints excluded: chain af residue 10 ILE Chi-restraints excluded: chain af residue 14 ARG Chi-restraints excluded: chain ag residue 36 LEU Chi-restraints excluded: chain aj residue 37 SER Chi-restraints excluded: chain aj residue 45 GLU Chi-restraints excluded: chain al residue 10 ILE Chi-restraints excluded: chain al residue 29 VAL Chi-restraints excluded: chain ba residue 15 GLU Chi-restraints excluded: chain ba residue 26 SER Chi-restraints excluded: chain bc residue 18 GLN Chi-restraints excluded: chain bd residue 26 SER Chi-restraints excluded: chain bd residue 40 LEU Chi-restraints excluded: chain bf residue 26 SER Chi-restraints excluded: chain bh residue 40 LEU Chi-restraints excluded: chain bi residue 19 GLU Chi-restraints excluded: chain bi residue 22 SER Chi-restraints excluded: chain bi residue 36 ILE Chi-restraints excluded: chain bj residue 44 ILE Chi-restraints excluded: chain bk residue 25 MET Chi-restraints excluded: chain bk residue 36 ILE Chi-restraints excluded: chain bl residue 40 LEU Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 163 LYS Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain l residue 82 LYS Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain ub residue 8 ILE Chi-restraints excluded: chain uu residue 6 GLU Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain x residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 0.6980 chunk 302 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 191 optimal weight: 0.7980 chunk 270 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 427 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 chunk 382 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 20 GLN AH 20 GLN ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS ** BJ 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 ASN X 58 GLN ae 20 GLN af 52 ASN ** ag 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** aj 42 ASN ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS ** bj 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** bk 21 HIS h 32 GLN m 188 ASN x 58 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 47562 Z= 0.185 Angle : 2.425 31.378 65208 Z= 0.821 Chirality : 0.037 0.190 6386 Planarity : 0.004 0.037 7950 Dihedral : 19.181 179.999 8630 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.89 % Allowed : 10.71 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.12), residues: 4532 helix: 2.44 (0.09), residues: 3020 sheet: 0.79 (0.69), residues: 44 loop : 0.37 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP m 157 HIS 0.010 0.001 HIS L 153 PHE 0.016 0.001 PHE H 20 TYR 0.022 0.001 TYRBM 24 ARG 0.004 0.000 ARGAE 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 651 time to evaluate : 4.938 Fit side-chains revert: symmetry clash REVERT: AA 3 LYS cc_start: 0.7670 (mttt) cc_final: 0.7070 (mptt) REVERT: AB 9 MET cc_start: 0.8363 (mtp) cc_final: 0.8130 (mtp) REVERT: AC 30 MET cc_start: 0.8369 (ttt) cc_final: 0.8117 (ttm) REVERT: AD 52 ASN cc_start: 0.7655 (m110) cc_final: 0.7240 (m110) REVERT: AE 17 PHE cc_start: 0.7869 (m-80) cc_final: 0.7597 (m-80) REVERT: AF 5 TYR cc_start: 0.6638 (p90) cc_final: 0.6254 (p90) REVERT: AI 9 MET cc_start: 0.6841 (mtp) cc_final: 0.6613 (mtm) REVERT: AJ 20 GLN cc_start: 0.7505 (tt0) cc_final: 0.7243 (tt0) REVERT: AJ 45 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: AK 11 PHE cc_start: 0.6558 (m-80) cc_final: 0.6319 (m-10) REVERT: AM 9 MET cc_start: 0.4268 (tpt) cc_final: 0.3587 (ptm) REVERT: AM 14 ARG cc_start: 0.4989 (mtm180) cc_final: 0.4520 (mtm180) REVERT: BA 15 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: BD 30 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8158 (tm) REVERT: BF 14 ASP cc_start: 0.6097 (t0) cc_final: 0.5802 (m-30) REVERT: BG 25 MET cc_start: 0.7363 (mmm) cc_final: 0.6908 (mmm) REVERT: BG 30 LEU cc_start: 0.8050 (tp) cc_final: 0.7785 (tp) REVERT: BH 29 TRP cc_start: 0.6770 (m100) cc_final: 0.6478 (m100) REVERT: BH 30 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6945 (mp) REVERT: BM 25 MET cc_start: 0.5851 (mmt) cc_final: 0.5510 (mmm) REVERT: BN 25 MET cc_start: 0.5007 (tpp) cc_final: 0.4637 (mmm) REVERT: H 52 ASN cc_start: 0.7842 (p0) cc_final: 0.7263 (t0) REVERT: L 91 ILE cc_start: 0.8922 (mt) cc_final: 0.8682 (mt) REVERT: L 202 LYS cc_start: 0.7525 (mmtt) cc_final: 0.7250 (mmmm) REVERT: L 248 MET cc_start: 0.8783 (mmm) cc_final: 0.8479 (mmm) REVERT: M 20 MET cc_start: 0.8234 (mmm) cc_final: 0.7961 (mmp) REVERT: M 26 LEU cc_start: 0.7789 (mt) cc_final: 0.7509 (tp) REVERT: M 61 PHE cc_start: 0.7390 (t80) cc_final: 0.6206 (m-10) REVERT: M 86 LEU cc_start: 0.8654 (tp) cc_final: 0.8406 (mm) REVERT: UU 36 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7912 (tp) REVERT: aa 3 LYS cc_start: 0.7865 (mttt) cc_final: 0.7312 (mptt) REVERT: ab 9 MET cc_start: 0.8260 (mtp) cc_final: 0.8015 (mtp) REVERT: ac 3 LYS cc_start: 0.7200 (mttt) cc_final: 0.6902 (mtmt) REVERT: ac 10 ILE cc_start: 0.8058 (mm) cc_final: 0.7805 (mt) REVERT: ac 30 MET cc_start: 0.8225 (ttt) cc_final: 0.7971 (ttm) REVERT: ad 52 ASN cc_start: 0.7608 (m110) cc_final: 0.7160 (m110) REVERT: ae 17 PHE cc_start: 0.7858 (m-80) cc_final: 0.7578 (m-80) REVERT: af 5 TYR cc_start: 0.6692 (p90) cc_final: 0.6309 (p90) REVERT: af 14 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6410 (mtp180) REVERT: ah 9 MET cc_start: 0.6329 (mtm) cc_final: 0.6079 (mtt) REVERT: ai 9 MET cc_start: 0.6821 (mtp) cc_final: 0.6591 (mtp) REVERT: ai 20 GLN cc_start: 0.7606 (tt0) cc_final: 0.7388 (pt0) REVERT: aj 20 GLN cc_start: 0.7589 (tt0) cc_final: 0.7329 (tt0) REVERT: aj 45 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: ak 11 PHE cc_start: 0.6611 (m-80) cc_final: 0.6362 (m-10) REVERT: am 9 MET cc_start: 0.4292 (tpt) cc_final: 0.3627 (ptm) REVERT: am 14 ARG cc_start: 0.4972 (mtm180) cc_final: 0.4535 (mtm180) REVERT: ba 15 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: bc 30 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8448 (tt) REVERT: bd 26 SER cc_start: 0.7914 (OUTLIER) cc_final: 0.7573 (t) REVERT: bf 14 ASP cc_start: 0.6086 (t0) cc_final: 0.5814 (m-30) REVERT: bg 25 MET cc_start: 0.7244 (mmm) cc_final: 0.6766 (mmm) REVERT: bg 30 LEU cc_start: 0.8077 (tp) cc_final: 0.7835 (tp) REVERT: bh 29 TRP cc_start: 0.6811 (m100) cc_final: 0.6510 (m100) REVERT: bm 25 MET cc_start: 0.5934 (mmt) cc_final: 0.5567 (mmm) REVERT: bn 25 MET cc_start: 0.5308 (tpp) cc_final: 0.4991 (mmm) REVERT: h 52 ASN cc_start: 0.7829 (p0) cc_final: 0.7258 (t0) REVERT: h 163 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7448 (pttp) REVERT: l 91 ILE cc_start: 0.8856 (mt) cc_final: 0.8630 (mt) REVERT: l 202 LYS cc_start: 0.7529 (mmtt) cc_final: 0.7270 (mmmm) REVERT: l 248 MET cc_start: 0.8792 (mmm) cc_final: 0.8489 (mmm) REVERT: m 20 MET cc_start: 0.8237 (mmm) cc_final: 0.7962 (mmp) REVERT: m 26 LEU cc_start: 0.7778 (mt) cc_final: 0.7507 (tp) REVERT: m 61 PHE cc_start: 0.7432 (t80) cc_final: 0.6225 (m-10) REVERT: m 86 LEU cc_start: 0.8651 (tp) cc_final: 0.8394 (mm) REVERT: uu 36 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7866 (tp) outliers start: 111 outliers final: 32 residues processed: 701 average time/residue: 1.3262 time to fit residues: 1192.4485 Evaluate side-chains 663 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 619 time to evaluate : 4.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 5 TYR Chi-restraints excluded: chain AF residue 10 ILE Chi-restraints excluded: chain AF residue 14 ARG Chi-restraints excluded: chain AJ residue 45 GLU Chi-restraints excluded: chain AK residue 47 SER Chi-restraints excluded: chain AM residue 34 ILE Chi-restraints excluded: chain BA residue 15 GLU Chi-restraints excluded: chain BA residue 26 SER Chi-restraints excluded: chain BD residue 26 SER Chi-restraints excluded: chain BD residue 30 LEU Chi-restraints excluded: chain BE residue 40 LEU Chi-restraints excluded: chain BH residue 30 LEU Chi-restraints excluded: chain BI residue 22 SER Chi-restraints excluded: chain BJ residue 44 ILE Chi-restraints excluded: chain BK residue 25 MET Chi-restraints excluded: chain BK residue 36 ILE Chi-restraints excluded: chain BL residue 40 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain UA residue 22 MET Chi-restraints excluded: chain UU residue 36 LEU Chi-restraints excluded: chain ad residue 9 MET Chi-restraints excluded: chain ae residue 5 TYR Chi-restraints excluded: chain af residue 10 ILE Chi-restraints excluded: chain af residue 14 ARG Chi-restraints excluded: chain ai residue 37 SER Chi-restraints excluded: chain aj residue 37 SER Chi-restraints excluded: chain aj residue 45 GLU Chi-restraints excluded: chain ak residue 47 SER Chi-restraints excluded: chain ba residue 15 GLU Chi-restraints excluded: chain ba residue 26 SER Chi-restraints excluded: chain bc residue 30 LEU Chi-restraints excluded: chain bd residue 26 SER Chi-restraints excluded: chain be residue 40 LEU Chi-restraints excluded: chain bi residue 22 SER Chi-restraints excluded: chain bj residue 44 ILE Chi-restraints excluded: chain bk residue 36 ILE Chi-restraints excluded: chain bl residue 40 LEU Chi-restraints excluded: chain h residue 163 LYS Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain ua residue 22 MET Chi-restraints excluded: chain uu residue 36 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 364 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 383 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 20 GLN ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS X 60 ASN ae 20 GLN af 52 ASN ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 47562 Z= 0.344 Angle : 2.476 29.385 65208 Z= 0.845 Chirality : 0.044 0.223 6386 Planarity : 0.005 0.043 7950 Dihedral : 19.740 179.994 8630 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.59 % Allowed : 11.15 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.12), residues: 4532 helix: 1.75 (0.09), residues: 3120 sheet: 0.58 (0.69), residues: 44 loop : -0.04 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP m 157 HIS 0.013 0.002 HIS M 182 PHE 0.023 0.002 PHEaa 25 TYR 0.023 0.002 TYRbm 24 ARG 0.004 0.001 ARGae 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 658 time to evaluate : 4.029 Fit side-chains revert: symmetry clash REVERT: AA 3 LYS cc_start: 0.7697 (mttt) cc_final: 0.7119 (mptt) REVERT: AA 14 ARG cc_start: 0.7217 (ttp-110) cc_final: 0.6991 (ttp80) REVERT: AC 15 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6364 (mtp-110) REVERT: AC 30 MET cc_start: 0.8388 (ttt) cc_final: 0.8116 (ttm) REVERT: AD 52 ASN cc_start: 0.7592 (m110) cc_final: 0.7171 (m110) REVERT: AE 7 ILE cc_start: 0.7744 (tp) cc_final: 0.7375 (pt) REVERT: AF 30 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7238 (tpt) REVERT: AG 36 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8724 (mt) REVERT: AH 33 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7883 (tt) REVERT: AI 9 MET cc_start: 0.6861 (mtp) cc_final: 0.6619 (mtm) REVERT: AJ 20 GLN cc_start: 0.7626 (tt0) cc_final: 0.7382 (tt0) REVERT: AJ 45 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: AK 11 PHE cc_start: 0.6680 (m-80) cc_final: 0.6469 (m-80) REVERT: AM 9 MET cc_start: 0.4252 (tpt) cc_final: 0.3626 (ptt) REVERT: AM 14 ARG cc_start: 0.5213 (mtm180) cc_final: 0.4780 (mtm180) REVERT: BD 10 THR cc_start: 0.8197 (p) cc_final: 0.7769 (m) REVERT: BD 30 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8300 (tm) REVERT: BG 30 LEU cc_start: 0.8094 (tp) cc_final: 0.7788 (tp) REVERT: BH 12 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6654 (mp) REVERT: BH 40 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8334 (tt) REVERT: BM 25 MET cc_start: 0.5844 (mmt) cc_final: 0.5534 (mmm) REVERT: BN 25 MET cc_start: 0.5104 (tpp) cc_final: 0.4692 (mmm) REVERT: BN 49 PHE cc_start: 0.5180 (OUTLIER) cc_final: 0.4785 (m-80) REVERT: H 52 ASN cc_start: 0.7853 (p0) cc_final: 0.7272 (t0) REVERT: H 159 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: H 184 LYS cc_start: 0.7011 (mmtt) cc_final: 0.6124 (mttt) REVERT: L 202 LYS cc_start: 0.7527 (mmtt) cc_final: 0.7286 (mmmm) REVERT: M 20 MET cc_start: 0.8246 (mmm) cc_final: 0.7969 (mmp) REVERT: M 26 LEU cc_start: 0.7831 (mt) cc_final: 0.7599 (tp) REVERT: M 86 LEU cc_start: 0.8717 (tp) cc_final: 0.8435 (mt) REVERT: X 58 GLN cc_start: 0.7084 (mp10) cc_final: 0.6751 (mp10) REVERT: X 59 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6521 (mp0) REVERT: X 60 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.6610 (m-40) REVERT: aa 3 LYS cc_start: 0.7812 (mttt) cc_final: 0.7471 (mtmm) REVERT: ac 3 LYS cc_start: 0.7357 (mttt) cc_final: 0.7033 (mtmt) REVERT: ac 9 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.6671 (mpt) REVERT: ac 10 ILE cc_start: 0.8103 (mm) cc_final: 0.7813 (mt) REVERT: ac 30 MET cc_start: 0.8221 (ttt) cc_final: 0.7914 (ttm) REVERT: ad 52 ASN cc_start: 0.7556 (m110) cc_final: 0.7120 (m110) REVERT: ae 7 ILE cc_start: 0.7718 (tp) cc_final: 0.7343 (pt) REVERT: af 14 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6424 (mtp-110) REVERT: ag 36 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8712 (mt) REVERT: ah 26 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8448 (mp) REVERT: ah 33 LEU cc_start: 0.8128 (tp) cc_final: 0.7865 (tt) REVERT: ai 9 MET cc_start: 0.6839 (mtp) cc_final: 0.6579 (mtp) REVERT: aj 20 GLN cc_start: 0.7733 (tt0) cc_final: 0.7441 (tt0) REVERT: aj 45 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: ak 11 PHE cc_start: 0.6651 (m-80) cc_final: 0.6394 (m-10) REVERT: am 9 MET cc_start: 0.4084 (tpt) cc_final: 0.3536 (ptt) REVERT: am 14 ARG cc_start: 0.5219 (mtm180) cc_final: 0.4750 (mtm180) REVERT: bd 10 THR cc_start: 0.8197 (p) cc_final: 0.7747 (m) REVERT: bd 26 SER cc_start: 0.7964 (OUTLIER) cc_final: 0.7616 (t) REVERT: bg 30 LEU cc_start: 0.8103 (tp) cc_final: 0.7806 (tp) REVERT: bh 40 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8394 (tt) REVERT: bm 25 MET cc_start: 0.5963 (mmt) cc_final: 0.5633 (mmm) REVERT: bn 25 MET cc_start: 0.5384 (tpp) cc_final: 0.5046 (mmm) REVERT: bn 49 PHE cc_start: 0.5208 (OUTLIER) cc_final: 0.4803 (m-80) REVERT: h 52 ASN cc_start: 0.7843 (p0) cc_final: 0.7257 (t0) REVERT: h 159 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: h 163 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7472 (pttp) REVERT: h 184 LYS cc_start: 0.6997 (mmtt) cc_final: 0.6082 (mttt) REVERT: l 202 LYS cc_start: 0.7532 (mmtt) cc_final: 0.7287 (mmmm) REVERT: m 20 MET cc_start: 0.8252 (mmm) cc_final: 0.7975 (mmp) REVERT: m 26 LEU cc_start: 0.7815 (mt) cc_final: 0.7588 (tp) REVERT: m 86 LEU cc_start: 0.8716 (tp) cc_final: 0.8429 (mt) REVERT: x 42 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7938 (mt) REVERT: x 59 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6430 (mp0) outliers start: 138 outliers final: 53 residues processed: 736 average time/residue: 1.3811 time to fit residues: 1312.7119 Evaluate side-chains 715 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 640 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 15 ARG Chi-restraints excluded: chain AE residue 5 TYR Chi-restraints excluded: chain AF residue 10 ILE Chi-restraints excluded: chain AF residue 14 ARG Chi-restraints excluded: chain AF residue 30 MET Chi-restraints excluded: chain AG residue 36 LEU Chi-restraints excluded: chain AH residue 33 LEU Chi-restraints excluded: chain AI residue 37 SER Chi-restraints excluded: chain AJ residue 33 LEU Chi-restraints excluded: chain AJ residue 37 SER Chi-restraints excluded: chain AJ residue 45 GLU Chi-restraints excluded: chain AK residue 47 SER Chi-restraints excluded: chain AL residue 29 VAL Chi-restraints excluded: chain BA residue 15 GLU Chi-restraints excluded: chain BA residue 26 SER Chi-restraints excluded: chain BD residue 26 SER Chi-restraints excluded: chain BD residue 30 LEU Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BE residue 14 ASP Chi-restraints excluded: chain BF residue 26 SER Chi-restraints excluded: chain BH residue 12 LEU Chi-restraints excluded: chain BH residue 40 LEU Chi-restraints excluded: chain BI residue 22 SER Chi-restraints excluded: chain BI residue 36 ILE Chi-restraints excluded: chain BJ residue 44 ILE Chi-restraints excluded: chain BK residue 25 MET Chi-restraints excluded: chain BK residue 36 ILE Chi-restraints excluded: chain BL residue 40 LEU Chi-restraints excluded: chain BN residue 49 PHE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain UA residue 22 MET Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain ac residue 9 MET Chi-restraints excluded: chain ae residue 5 TYR Chi-restraints excluded: chain af residue 10 ILE Chi-restraints excluded: chain af residue 14 ARG Chi-restraints excluded: chain ag residue 36 LEU Chi-restraints excluded: chain ah residue 26 LEU Chi-restraints excluded: chain ai residue 37 SER Chi-restraints excluded: chain aj residue 37 SER Chi-restraints excluded: chain aj residue 45 GLU Chi-restraints excluded: chain ak residue 47 SER Chi-restraints excluded: chain al residue 10 ILE Chi-restraints excluded: chain al residue 29 VAL Chi-restraints excluded: chain ba residue 15 GLU Chi-restraints excluded: chain ba residue 26 SER Chi-restraints excluded: chain bd residue 26 SER Chi-restraints excluded: chain bd residue 40 LEU Chi-restraints excluded: chain be residue 14 ASP Chi-restraints excluded: chain bf residue 26 SER Chi-restraints excluded: chain bh residue 40 LEU Chi-restraints excluded: chain bi residue 22 SER Chi-restraints excluded: chain bi residue 36 ILE Chi-restraints excluded: chain bj residue 44 ILE Chi-restraints excluded: chain bk residue 36 ILE Chi-restraints excluded: chain bl residue 40 LEU Chi-restraints excluded: chain bn residue 49 PHE Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 159 GLU Chi-restraints excluded: chain h residue 163 LYS Chi-restraints excluded: chain h residue 231 ASP Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain ua residue 22 MET Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain x residue 28 MET Chi-restraints excluded: chain x residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 5.9990 chunk 384 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 427 optimal weight: 4.9990 chunk 355 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 20 GLN ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 42 ASN ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS M 188 ASN ae 20 GLN af 52 ASN ** ag 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ak 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS m 188 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 47562 Z= 0.181 Angle : 2.362 27.556 65208 Z= 0.800 Chirality : 0.037 0.172 6386 Planarity : 0.004 0.041 7950 Dihedral : 18.995 179.940 8630 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.63 % Allowed : 12.69 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.12), residues: 4532 helix: 2.59 (0.09), residues: 2994 sheet: 0.75 (0.68), residues: 44 loop : 0.26 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAH 8 HIS 0.012 0.001 HISbl 21 PHE 0.019 0.001 PHEAN 25 TYR 0.025 0.001 TYRBM 24 ARG 0.006 0.000 ARGag 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 654 time to evaluate : 4.594 Fit side-chains revert: symmetry clash REVERT: AA 3 LYS cc_start: 0.7640 (mttt) cc_final: 0.7090 (mptt) REVERT: AC 15 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6997 (ttt-90) REVERT: AC 30 MET cc_start: 0.8366 (ttt) cc_final: 0.8106 (ttm) REVERT: AD 52 ASN cc_start: 0.7652 (m110) cc_final: 0.7209 (m110) REVERT: AE 17 PHE cc_start: 0.7876 (m-80) cc_final: 0.7596 (m-80) REVERT: AF 30 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7241 (tpt) REVERT: AI 9 MET cc_start: 0.6809 (mtp) cc_final: 0.6556 (mtm) REVERT: AJ 45 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: AM 9 MET cc_start: 0.3934 (tpt) cc_final: 0.3458 (ptm) REVERT: AM 14 ARG cc_start: 0.5012 (mtm180) cc_final: 0.4576 (mtm180) REVERT: BA 15 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: BD 30 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8200 (tm) REVERT: BG 25 MET cc_start: 0.7301 (mmm) cc_final: 0.6900 (mmm) REVERT: BG 30 LEU cc_start: 0.8044 (tp) cc_final: 0.7784 (tp) REVERT: BH 29 TRP cc_start: 0.6790 (m100) cc_final: 0.6537 (m100) REVERT: BM 24 TYR cc_start: 0.5944 (t80) cc_final: 0.5589 (t80) REVERT: BM 25 MET cc_start: 0.5803 (mmt) cc_final: 0.5462 (mmm) REVERT: BN 25 MET cc_start: 0.4920 (tpp) cc_final: 0.4590 (mmm) REVERT: BN 49 PHE cc_start: 0.5064 (OUTLIER) cc_final: 0.4807 (m-80) REVERT: H 52 ASN cc_start: 0.7841 (p0) cc_final: 0.7272 (t0) REVERT: L 47 ILE cc_start: 0.8670 (mm) cc_final: 0.8460 (mt) REVERT: L 91 ILE cc_start: 0.8927 (mt) cc_final: 0.8689 (mt) REVERT: L 202 LYS cc_start: 0.7429 (mmtt) cc_final: 0.7168 (mmmm) REVERT: L 248 MET cc_start: 0.8749 (mmm) cc_final: 0.8526 (mmm) REVERT: M 20 MET cc_start: 0.8219 (mmm) cc_final: 0.7970 (mmp) REVERT: M 26 LEU cc_start: 0.7794 (mt) cc_final: 0.7513 (tp) REVERT: M 61 PHE cc_start: 0.7394 (t80) cc_final: 0.6247 (m-10) REVERT: M 86 LEU cc_start: 0.8674 (tp) cc_final: 0.8422 (mm) REVERT: M 216 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.7796 (t80) REVERT: UU 6 GLU cc_start: 0.4766 (OUTLIER) cc_final: 0.4394 (mt-10) REVERT: aa 3 LYS cc_start: 0.7820 (mttt) cc_final: 0.7353 (mptt) REVERT: ac 3 LYS cc_start: 0.7218 (mttt) cc_final: 0.6904 (mtmt) REVERT: ac 10 ILE cc_start: 0.8050 (mm) cc_final: 0.7785 (mt) REVERT: ac 30 MET cc_start: 0.8234 (ttt) cc_final: 0.7948 (ttm) REVERT: ad 9 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7604 (mpp) REVERT: ad 52 ASN cc_start: 0.7618 (m110) cc_final: 0.7154 (m110) REVERT: ae 3 LYS cc_start: 0.6683 (mttm) cc_final: 0.6454 (mttm) REVERT: af 14 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6422 (mtp-110) REVERT: ah 33 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7787 (tt) REVERT: ai 9 MET cc_start: 0.6775 (mtp) cc_final: 0.6523 (mtm) REVERT: aj 20 GLN cc_start: 0.7575 (tt0) cc_final: 0.7338 (tt0) REVERT: aj 45 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6540 (mp0) REVERT: ak 9 MET cc_start: 0.5119 (mpt) cc_final: 0.4912 (mmt) REVERT: ak 11 PHE cc_start: 0.6622 (m-80) cc_final: 0.6371 (m-10) REVERT: am 9 MET cc_start: 0.3871 (tpt) cc_final: 0.3511 (ptt) REVERT: am 14 ARG cc_start: 0.4982 (mtm180) cc_final: 0.4582 (mtm180) REVERT: ba 15 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: bd 26 SER cc_start: 0.7910 (OUTLIER) cc_final: 0.7583 (t) REVERT: bg 25 MET cc_start: 0.7169 (mmm) cc_final: 0.6710 (mmm) REVERT: bg 30 LEU cc_start: 0.8061 (tp) cc_final: 0.7802 (tp) REVERT: bh 29 TRP cc_start: 0.6799 (m100) cc_final: 0.6531 (m100) REVERT: bm 24 TYR cc_start: 0.6001 (t80) cc_final: 0.5633 (t80) REVERT: bm 25 MET cc_start: 0.5927 (mmt) cc_final: 0.5590 (mmm) REVERT: bn 25 MET cc_start: 0.5222 (tpp) cc_final: 0.4932 (mmm) REVERT: bn 49 PHE cc_start: 0.5122 (OUTLIER) cc_final: 0.4850 (m-80) REVERT: h 52 ASN cc_start: 0.7844 (p0) cc_final: 0.7258 (t0) REVERT: h 154 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7445 (ttp-170) REVERT: h 163 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7493 (pttp) REVERT: l 47 ILE cc_start: 0.8663 (mm) cc_final: 0.8456 (mt) REVERT: l 91 ILE cc_start: 0.8861 (mt) cc_final: 0.8658 (mt) REVERT: l 202 LYS cc_start: 0.7431 (mmtt) cc_final: 0.7175 (mmmm) REVERT: l 248 MET cc_start: 0.8759 (mmm) cc_final: 0.8540 (mmm) REVERT: m 20 MET cc_start: 0.8220 (mmm) cc_final: 0.7969 (mmp) REVERT: m 26 LEU cc_start: 0.7792 (mt) cc_final: 0.7518 (tp) REVERT: m 61 PHE cc_start: 0.7433 (t80) cc_final: 0.6251 (m-10) REVERT: m 86 LEU cc_start: 0.8673 (tp) cc_final: 0.8412 (mm) REVERT: m 216 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.7801 (t80) REVERT: uu 6 GLU cc_start: 0.4864 (OUTLIER) cc_final: 0.4554 (mt-10) REVERT: x 59 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6311 (mp0) outliers start: 101 outliers final: 40 residues processed: 706 average time/residue: 1.3132 time to fit residues: 1184.0985 Evaluate side-chains 689 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 631 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 15 ARG Chi-restraints excluded: chain AE residue 5 TYR Chi-restraints excluded: chain AF residue 10 ILE Chi-restraints excluded: chain AF residue 14 ARG Chi-restraints excluded: chain AF residue 30 MET Chi-restraints excluded: chain AG residue 12 ASP Chi-restraints excluded: chain AI residue 10 ILE Chi-restraints excluded: chain AJ residue 37 SER Chi-restraints excluded: chain AJ residue 45 GLU Chi-restraints excluded: chain AK residue 47 SER Chi-restraints excluded: chain BA residue 15 GLU Chi-restraints excluded: chain BA residue 26 SER Chi-restraints excluded: chain BD residue 26 SER Chi-restraints excluded: chain BD residue 30 LEU Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BE residue 40 LEU Chi-restraints excluded: chain BF residue 26 SER Chi-restraints excluded: chain BJ residue 44 ILE Chi-restraints excluded: chain BK residue 25 MET Chi-restraints excluded: chain BK residue 36 ILE Chi-restraints excluded: chain BL residue 40 LEU Chi-restraints excluded: chain BN residue 49 PHE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain UA residue 19 PHE Chi-restraints excluded: chain UA residue 22 MET Chi-restraints excluded: chain UU residue 6 GLU Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain ad residue 9 MET Chi-restraints excluded: chain ae residue 5 TYR Chi-restraints excluded: chain af residue 10 ILE Chi-restraints excluded: chain af residue 14 ARG Chi-restraints excluded: chain ah residue 33 LEU Chi-restraints excluded: chain ai residue 10 ILE Chi-restraints excluded: chain ai residue 37 SER Chi-restraints excluded: chain aj residue 37 SER Chi-restraints excluded: chain aj residue 45 GLU Chi-restraints excluded: chain ak residue 47 SER Chi-restraints excluded: chain ba residue 15 GLU Chi-restraints excluded: chain ba residue 26 SER Chi-restraints excluded: chain bd residue 26 SER Chi-restraints excluded: chain bd residue 40 LEU Chi-restraints excluded: chain be residue 40 LEU Chi-restraints excluded: chain bf residue 26 SER Chi-restraints excluded: chain bj residue 44 ILE Chi-restraints excluded: chain bk residue 36 ILE Chi-restraints excluded: chain bl residue 40 LEU Chi-restraints excluded: chain bn residue 49 PHE Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 163 LYS Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain ua residue 19 PHE Chi-restraints excluded: chain ua residue 22 MET Chi-restraints excluded: chain uu residue 6 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 359 optimal weight: 0.0970 chunk 238 optimal weight: 4.9990 chunk 426 optimal weight: 3.9990 chunk 266 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 20 GLN AE 20 GLN ** AG 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS X 60 ASN ae 20 GLN af 52 ASN ** ag 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ak 20 GLN ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 47562 Z= 0.270 Angle : 2.388 27.595 65208 Z= 0.813 Chirality : 0.040 0.203 6386 Planarity : 0.004 0.041 7950 Dihedral : 19.222 180.000 8630 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.07 % Allowed : 12.77 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.12), residues: 4532 helix: 2.27 (0.09), residues: 3038 sheet: 0.57 (0.69), residues: 44 loop : 0.14 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 157 HIS 0.014 0.002 HISBL 21 PHE 0.020 0.002 PHEAN 25 TYR 0.023 0.002 TYRae 5 ARG 0.004 0.000 ARGAE 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 641 time to evaluate : 4.408 Fit side-chains revert: symmetry clash REVERT: AA 3 LYS cc_start: 0.7680 (mttt) cc_final: 0.7215 (mttp) REVERT: AC 9 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.6540 (mpt) REVERT: AC 15 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6363 (mtp-110) REVERT: AC 30 MET cc_start: 0.8391 (ttt) cc_final: 0.8128 (ttm) REVERT: AD 52 ASN cc_start: 0.7631 (m110) cc_final: 0.7194 (m110) REVERT: AF 30 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7246 (tpt) REVERT: AH 26 LEU cc_start: 0.8562 (mt) cc_final: 0.8351 (mp) REVERT: AH 33 LEU cc_start: 0.8174 (tp) cc_final: 0.7944 (tt) REVERT: AI 9 MET cc_start: 0.6840 (mtp) cc_final: 0.6578 (mtm) REVERT: AJ 45 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: AM 9 MET cc_start: 0.3958 (tpt) cc_final: 0.3476 (ptt) REVERT: AM 14 ARG cc_start: 0.5099 (mtm180) cc_final: 0.4684 (mtm180) REVERT: BA 15 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: BD 30 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8298 (tm) REVERT: BF 36 ILE cc_start: 0.8209 (mt) cc_final: 0.7934 (tt) REVERT: BG 25 MET cc_start: 0.7288 (mmm) cc_final: 0.6875 (mmm) REVERT: BG 30 LEU cc_start: 0.8097 (tp) cc_final: 0.7707 (tp) REVERT: BH 29 TRP cc_start: 0.6809 (m100) cc_final: 0.6545 (m100) REVERT: BH 40 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8328 (tt) REVERT: BM 25 MET cc_start: 0.5850 (mmt) cc_final: 0.5546 (mmm) REVERT: BN 25 MET cc_start: 0.4982 (tpp) cc_final: 0.4572 (mmm) REVERT: BN 49 PHE cc_start: 0.5066 (OUTLIER) cc_final: 0.4736 (m-80) REVERT: H 52 ASN cc_start: 0.7835 (p0) cc_final: 0.7255 (t0) REVERT: H 159 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: H 184 LYS cc_start: 0.6963 (mmtt) cc_final: 0.6131 (mttt) REVERT: L 202 LYS cc_start: 0.7503 (mmtt) cc_final: 0.7257 (mmmm) REVERT: M 20 MET cc_start: 0.8226 (mmm) cc_final: 0.7966 (mmp) REVERT: M 26 LEU cc_start: 0.7817 (mt) cc_final: 0.7571 (tp) REVERT: M 61 PHE cc_start: 0.7416 (t80) cc_final: 0.6236 (m-10) REVERT: M 86 LEU cc_start: 0.8692 (tp) cc_final: 0.8413 (mm) REVERT: M 216 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.7976 (t80) REVERT: UU 6 GLU cc_start: 0.4823 (OUTLIER) cc_final: 0.4401 (mt-10) REVERT: X 60 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.6592 (m-40) REVERT: aa 3 LYS cc_start: 0.7803 (mttt) cc_final: 0.7366 (mttp) REVERT: ac 9 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.6657 (mpt) REVERT: ac 10 ILE cc_start: 0.8069 (mm) cc_final: 0.7791 (mt) REVERT: ac 30 MET cc_start: 0.8238 (ttt) cc_final: 0.7965 (ttm) REVERT: ad 52 ASN cc_start: 0.7597 (m110) cc_final: 0.7144 (m110) REVERT: ae 3 LYS cc_start: 0.6687 (mttm) cc_final: 0.6169 (mmtp) REVERT: af 14 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.6482 (mtp-110) REVERT: af 30 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6891 (tpt) REVERT: ah 33 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7904 (tt) REVERT: ai 9 MET cc_start: 0.6823 (mtp) cc_final: 0.6560 (mtm) REVERT: aj 20 GLN cc_start: 0.7662 (tt0) cc_final: 0.7388 (tt0) REVERT: aj 45 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: ak 9 MET cc_start: 0.5073 (mpt) cc_final: 0.4830 (mmt) REVERT: ak 11 PHE cc_start: 0.6639 (m-80) cc_final: 0.6397 (m-10) REVERT: am 9 MET cc_start: 0.3936 (tpt) cc_final: 0.3522 (ptt) REVERT: am 14 ARG cc_start: 0.5132 (mtm180) cc_final: 0.4677 (mtm180) REVERT: bd 26 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7600 (t) REVERT: bf 36 ILE cc_start: 0.8212 (mt) cc_final: 0.7941 (tt) REVERT: bg 25 MET cc_start: 0.7182 (mmm) cc_final: 0.6749 (mmm) REVERT: bg 30 LEU cc_start: 0.8092 (tp) cc_final: 0.7712 (tp) REVERT: bh 29 TRP cc_start: 0.6793 (m100) cc_final: 0.6536 (m100) REVERT: bm 25 MET cc_start: 0.5936 (mmt) cc_final: 0.5626 (mmm) REVERT: bn 25 MET cc_start: 0.5283 (tpp) cc_final: 0.4928 (mmm) REVERT: bn 49 PHE cc_start: 0.5120 (OUTLIER) cc_final: 0.4775 (m-80) REVERT: h 52 ASN cc_start: 0.7837 (p0) cc_final: 0.7246 (t0) REVERT: h 159 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: h 163 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7485 (pttp) REVERT: h 184 LYS cc_start: 0.6953 (mmtt) cc_final: 0.6078 (mttt) REVERT: l 202 LYS cc_start: 0.7503 (mmtt) cc_final: 0.7261 (mmmm) REVERT: m 20 MET cc_start: 0.8229 (mmm) cc_final: 0.7969 (mmp) REVERT: m 26 LEU cc_start: 0.7807 (mt) cc_final: 0.7566 (tp) REVERT: m 61 PHE cc_start: 0.7459 (t80) cc_final: 0.6273 (m-10) REVERT: m 86 LEU cc_start: 0.8684 (tp) cc_final: 0.8397 (mm) REVERT: m 216 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.7973 (t80) REVERT: uu 6 GLU cc_start: 0.4919 (OUTLIER) cc_final: 0.4561 (mt-10) REVERT: x 42 LEU cc_start: 0.8362 (tp) cc_final: 0.7890 (mt) REVERT: x 59 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6325 (mp0) outliers start: 118 outliers final: 52 residues processed: 712 average time/residue: 1.3657 time to fit residues: 1238.5534 Evaluate side-chains 704 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 629 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 9 MET Chi-restraints excluded: chain AC residue 15 ARG Chi-restraints excluded: chain AE residue 5 TYR Chi-restraints excluded: chain AF residue 10 ILE Chi-restraints excluded: chain AF residue 14 ARG Chi-restraints excluded: chain AF residue 30 MET Chi-restraints excluded: chain AI residue 10 ILE Chi-restraints excluded: chain AI residue 37 SER Chi-restraints excluded: chain AJ residue 33 LEU Chi-restraints excluded: chain AJ residue 37 SER Chi-restraints excluded: chain AJ residue 45 GLU Chi-restraints excluded: chain AK residue 47 SER Chi-restraints excluded: chain AN residue 30 MET Chi-restraints excluded: chain BA residue 15 GLU Chi-restraints excluded: chain BA residue 26 SER Chi-restraints excluded: chain BD residue 26 SER Chi-restraints excluded: chain BD residue 30 LEU Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BE residue 14 ASP Chi-restraints excluded: chain BF residue 26 SER Chi-restraints excluded: chain BH residue 40 LEU Chi-restraints excluded: chain BI residue 22 SER Chi-restraints excluded: chain BI residue 36 ILE Chi-restraints excluded: chain BJ residue 44 ILE Chi-restraints excluded: chain BK residue 25 MET Chi-restraints excluded: chain BK residue 36 ILE Chi-restraints excluded: chain BL residue 40 LEU Chi-restraints excluded: chain BN residue 49 PHE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain UA residue 19 PHE Chi-restraints excluded: chain UA residue 22 MET Chi-restraints excluded: chain UU residue 6 GLU Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain ac residue 9 MET Chi-restraints excluded: chain ad residue 9 MET Chi-restraints excluded: chain ae residue 5 TYR Chi-restraints excluded: chain af residue 10 ILE Chi-restraints excluded: chain af residue 14 ARG Chi-restraints excluded: chain af residue 30 MET Chi-restraints excluded: chain ah residue 33 LEU Chi-restraints excluded: chain ai residue 10 ILE Chi-restraints excluded: chain ai residue 37 SER Chi-restraints excluded: chain aj residue 37 SER Chi-restraints excluded: chain aj residue 45 GLU Chi-restraints excluded: chain ak residue 47 SER Chi-restraints excluded: chain an residue 30 MET Chi-restraints excluded: chain ba residue 15 GLU Chi-restraints excluded: chain ba residue 26 SER Chi-restraints excluded: chain bd residue 26 SER Chi-restraints excluded: chain bd residue 40 LEU Chi-restraints excluded: chain be residue 14 ASP Chi-restraints excluded: chain bf residue 26 SER Chi-restraints excluded: chain bi residue 22 SER Chi-restraints excluded: chain bj residue 44 ILE Chi-restraints excluded: chain bk residue 36 ILE Chi-restraints excluded: chain bl residue 40 LEU Chi-restraints excluded: chain bn residue 49 PHE Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 159 GLU Chi-restraints excluded: chain h residue 163 LYS Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 216 PHE Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain ua residue 19 PHE Chi-restraints excluded: chain ua residue 22 MET Chi-restraints excluded: chain uu residue 6 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 254 optimal weight: 7.9990 chunk 128 optimal weight: 0.3980 chunk 83 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 334 optimal weight: 2.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 20 GLN AE 20 GLN ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BF 18 GLN BG 21 HIS M 188 ASN X 18 ASN X 60 ASN ae 20 GLN af 52 ASN ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 47562 Z= 0.349 Angle : 2.416 28.040 65208 Z= 0.826 Chirality : 0.044 0.225 6386 Planarity : 0.005 0.044 7950 Dihedral : 19.625 179.994 8630 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.09 % Allowed : 13.18 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.12), residues: 4532 helix: 1.93 (0.09), residues: 3032 sheet: 0.46 (0.68), residues: 44 loop : -0.08 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPAF 8 HIS 0.015 0.002 HISBL 21 PHE 0.022 0.002 PHEAN 25 TYR 0.025 0.002 TYRae 5 ARG 0.005 0.001 ARGae 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 649 time to evaluate : 4.827 Fit side-chains revert: symmetry clash REVERT: AA 3 LYS cc_start: 0.7721 (mttt) cc_final: 0.7257 (mttp) REVERT: AC 9 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.6547 (mpt) REVERT: AC 15 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6386 (mtp-110) REVERT: AC 30 MET cc_start: 0.8399 (ttt) cc_final: 0.8113 (ttm) REVERT: AD 52 ASN cc_start: 0.7610 (m110) cc_final: 0.7180 (m110) REVERT: AE 7 ILE cc_start: 0.7750 (tp) cc_final: 0.7370 (pt) REVERT: AF 30 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7233 (tpt) REVERT: AG 36 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8705 (mt) REVERT: AH 26 LEU cc_start: 0.8577 (mt) cc_final: 0.8371 (mp) REVERT: AH 33 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7961 (tt) REVERT: AI 9 MET cc_start: 0.6836 (mtp) cc_final: 0.6575 (mtm) REVERT: AJ 45 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6549 (mp0) REVERT: AM 14 ARG cc_start: 0.5210 (mtm180) cc_final: 0.4791 (mtm180) REVERT: BD 10 THR cc_start: 0.8201 (p) cc_final: 0.7755 (m) REVERT: BD 30 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8325 (tm) REVERT: BG 25 MET cc_start: 0.7286 (mmm) cc_final: 0.6873 (mmm) REVERT: BG 30 LEU cc_start: 0.8054 (tp) cc_final: 0.7731 (tp) REVERT: BH 40 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8332 (tt) REVERT: BM 25 MET cc_start: 0.5870 (mmt) cc_final: 0.5575 (mmm) REVERT: BN 25 MET cc_start: 0.5059 (tpp) cc_final: 0.4672 (mmm) REVERT: BN 49 PHE cc_start: 0.5205 (OUTLIER) cc_final: 0.4795 (m-80) REVERT: H 52 ASN cc_start: 0.7831 (p0) cc_final: 0.7318 (t0) REVERT: H 159 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: H 184 LYS cc_start: 0.7010 (mmtt) cc_final: 0.6125 (mttt) REVERT: L 202 LYS cc_start: 0.7527 (mmtt) cc_final: 0.7279 (mmmm) REVERT: M 20 MET cc_start: 0.8230 (mmm) cc_final: 0.7959 (mmp) REVERT: M 26 LEU cc_start: 0.7845 (mt) cc_final: 0.7598 (tp) REVERT: M 86 LEU cc_start: 0.8722 (tp) cc_final: 0.8435 (mt) REVERT: UU 6 GLU cc_start: 0.4851 (OUTLIER) cc_final: 0.4405 (mt-10) REVERT: X 60 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7414 (m110) REVERT: aa 3 LYS cc_start: 0.7815 (mttt) cc_final: 0.7397 (mttp) REVERT: ac 9 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.6638 (mpt) REVERT: ac 10 ILE cc_start: 0.8080 (mm) cc_final: 0.7811 (mt) REVERT: ac 30 MET cc_start: 0.8239 (ttt) cc_final: 0.7960 (ttm) REVERT: ad 52 ASN cc_start: 0.7580 (m110) cc_final: 0.7116 (m110) REVERT: ae 7 ILE cc_start: 0.7723 (tp) cc_final: 0.7347 (pt) REVERT: af 30 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6883 (tpt) REVERT: ag 36 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8726 (mt) REVERT: ah 33 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8036 (tt) REVERT: ai 9 MET cc_start: 0.6822 (mtp) cc_final: 0.6564 (mtm) REVERT: aj 20 GLN cc_start: 0.7719 (tt0) cc_final: 0.7443 (tt0) REVERT: aj 45 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: ak 9 MET cc_start: 0.5055 (mpt) cc_final: 0.4830 (mmt) REVERT: ak 11 PHE cc_start: 0.6657 (m-80) cc_final: 0.6438 (m-80) REVERT: ak 53 ARG cc_start: 0.7357 (mtt180) cc_final: 0.7154 (mtt180) REVERT: am 14 ARG cc_start: 0.5203 (mtm180) cc_final: 0.4748 (mtm180) REVERT: bd 10 THR cc_start: 0.8200 (p) cc_final: 0.7752 (m) REVERT: bd 26 SER cc_start: 0.7939 (OUTLIER) cc_final: 0.7595 (t) REVERT: bg 25 MET cc_start: 0.7185 (mmm) cc_final: 0.6713 (mmm) REVERT: bg 30 LEU cc_start: 0.8069 (tp) cc_final: 0.7754 (tp) REVERT: bh 40 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8380 (tt) REVERT: bm 25 MET cc_start: 0.5920 (mmt) cc_final: 0.5625 (mmm) REVERT: bn 25 MET cc_start: 0.5359 (tpp) cc_final: 0.5038 (mmm) REVERT: bn 49 PHE cc_start: 0.5233 (OUTLIER) cc_final: 0.4827 (m-80) REVERT: h 52 ASN cc_start: 0.7838 (p0) cc_final: 0.7311 (t0) REVERT: h 159 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: h 163 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7482 (pttp) REVERT: h 184 LYS cc_start: 0.7040 (mmtt) cc_final: 0.6052 (mttt) REVERT: l 202 LYS cc_start: 0.7523 (mmtt) cc_final: 0.7281 (mmmm) REVERT: m 20 MET cc_start: 0.8233 (mmm) cc_final: 0.7958 (mmp) REVERT: m 26 LEU cc_start: 0.7830 (mt) cc_final: 0.7591 (tp) REVERT: m 86 LEU cc_start: 0.8719 (tp) cc_final: 0.8422 (mt) REVERT: uu 6 GLU cc_start: 0.4944 (OUTLIER) cc_final: 0.4563 (mt-10) REVERT: x 42 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7910 (mt) REVERT: x 58 GLN cc_start: 0.7066 (mp10) cc_final: 0.6714 (mp10) outliers start: 119 outliers final: 60 residues processed: 720 average time/residue: 1.3273 time to fit residues: 1218.5783 Evaluate side-chains 716 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 632 time to evaluate : 4.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 9 MET Chi-restraints excluded: chain AC residue 15 ARG Chi-restraints excluded: chain AE residue 5 TYR Chi-restraints excluded: chain AF residue 10 ILE Chi-restraints excluded: chain AF residue 14 ARG Chi-restraints excluded: chain AF residue 30 MET Chi-restraints excluded: chain AG residue 36 LEU Chi-restraints excluded: chain AH residue 33 LEU Chi-restraints excluded: chain AI residue 10 ILE Chi-restraints excluded: chain AI residue 37 SER Chi-restraints excluded: chain AJ residue 33 LEU Chi-restraints excluded: chain AJ residue 37 SER Chi-restraints excluded: chain AJ residue 45 GLU Chi-restraints excluded: chain AK residue 47 SER Chi-restraints excluded: chain AL residue 2 SER Chi-restraints excluded: chain AN residue 34 ILE Chi-restraints excluded: chain BA residue 15 GLU Chi-restraints excluded: chain BA residue 26 SER Chi-restraints excluded: chain BD residue 26 SER Chi-restraints excluded: chain BD residue 30 LEU Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BE residue 14 ASP Chi-restraints excluded: chain BF residue 26 SER Chi-restraints excluded: chain BH residue 40 LEU Chi-restraints excluded: chain BI residue 22 SER Chi-restraints excluded: chain BI residue 36 ILE Chi-restraints excluded: chain BJ residue 44 ILE Chi-restraints excluded: chain BK residue 25 MET Chi-restraints excluded: chain BK residue 36 ILE Chi-restraints excluded: chain BL residue 40 LEU Chi-restraints excluded: chain BN residue 49 PHE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain UA residue 19 PHE Chi-restraints excluded: chain UA residue 22 MET Chi-restraints excluded: chain UU residue 6 GLU Chi-restraints excluded: chain X residue 28 MET Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain ac residue 9 MET Chi-restraints excluded: chain ad residue 9 MET Chi-restraints excluded: chain ae residue 5 TYR Chi-restraints excluded: chain af residue 10 ILE Chi-restraints excluded: chain af residue 30 MET Chi-restraints excluded: chain ag residue 36 LEU Chi-restraints excluded: chain ah residue 33 LEU Chi-restraints excluded: chain ai residue 10 ILE Chi-restraints excluded: chain ai residue 37 SER Chi-restraints excluded: chain aj residue 37 SER Chi-restraints excluded: chain aj residue 45 GLU Chi-restraints excluded: chain ak residue 47 SER Chi-restraints excluded: chain al residue 2 SER Chi-restraints excluded: chain al residue 29 VAL Chi-restraints excluded: chain an residue 30 MET Chi-restraints excluded: chain ba residue 15 GLU Chi-restraints excluded: chain ba residue 26 SER Chi-restraints excluded: chain bd residue 26 SER Chi-restraints excluded: chain bd residue 40 LEU Chi-restraints excluded: chain be residue 14 ASP Chi-restraints excluded: chain bf residue 26 SER Chi-restraints excluded: chain bh residue 40 LEU Chi-restraints excluded: chain bi residue 22 SER Chi-restraints excluded: chain bj residue 44 ILE Chi-restraints excluded: chain bk residue 36 ILE Chi-restraints excluded: chain bl residue 40 LEU Chi-restraints excluded: chain bn residue 49 PHE Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 159 GLU Chi-restraints excluded: chain h residue 163 LYS Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain ua residue 19 PHE Chi-restraints excluded: chain ua residue 22 MET Chi-restraints excluded: chain uu residue 6 GLU Chi-restraints excluded: chain x residue 21 LEU Chi-restraints excluded: chain x residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 1.9990 chunk 408 optimal weight: 1.9990 chunk 372 optimal weight: 1.9990 chunk 396 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 311 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 358 optimal weight: 0.0040 chunk 375 optimal weight: 0.6980 chunk 395 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 20 GLN ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS M 188 ASN M 300 ASN X 60 ASN aa 20 GLN ae 20 GLN ** al 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bf 18 GLN bg 21 HIS m 188 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47562 Z= 0.198 Angle : 2.335 26.502 65208 Z= 0.793 Chirality : 0.038 0.179 6386 Planarity : 0.004 0.044 7950 Dihedral : 19.134 179.971 8630 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.34 % Allowed : 14.09 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.12), residues: 4532 helix: 2.43 (0.09), residues: 3016 sheet: 1.63 (1.00), residues: 24 loop : 0.04 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPBJ 29 HIS 0.013 0.001 HISBL 21 PHE 0.023 0.001 PHEAN 25 TYR 0.023 0.001 TYRae 5 ARG 0.003 0.000 ARGal 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 643 time to evaluate : 4.314 Fit side-chains revert: symmetry clash REVERT: AA 3 LYS cc_start: 0.7657 (mttt) cc_final: 0.7162 (mttp) REVERT: AC 30 MET cc_start: 0.8405 (ttt) cc_final: 0.8122 (ttm) REVERT: AD 52 ASN cc_start: 0.7651 (m110) cc_final: 0.7213 (m110) REVERT: AF 30 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7248 (tpt) REVERT: AG 36 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8665 (mt) REVERT: AH 26 LEU cc_start: 0.8525 (mt) cc_final: 0.8313 (mp) REVERT: AH 33 LEU cc_start: 0.8187 (tp) cc_final: 0.7941 (tt) REVERT: AI 6 LYS cc_start: 0.7124 (mptp) cc_final: 0.6914 (mptp) REVERT: AI 9 MET cc_start: 0.6877 (mtp) cc_final: 0.6664 (mtp) REVERT: AJ 45 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: AM 14 ARG cc_start: 0.5027 (mtm180) cc_final: 0.4632 (mtm180) REVERT: AN 40 SER cc_start: 0.4981 (p) cc_final: 0.4374 (t) REVERT: BA 15 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: BD 30 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8244 (tm) REVERT: BF 36 ILE cc_start: 0.8194 (mt) cc_final: 0.7929 (tt) REVERT: BG 25 MET cc_start: 0.7242 (mmm) cc_final: 0.6830 (mmm) REVERT: BG 30 LEU cc_start: 0.8014 (tp) cc_final: 0.7725 (tp) REVERT: BH 29 TRP cc_start: 0.6784 (m100) cc_final: 0.6542 (m100) REVERT: BM 25 MET cc_start: 0.5817 (mmt) cc_final: 0.5561 (mmm) REVERT: BN 25 MET cc_start: 0.4925 (tpp) cc_final: 0.4568 (mmm) REVERT: BN 49 PHE cc_start: 0.5035 (OUTLIER) cc_final: 0.4787 (m-80) REVERT: H 52 ASN cc_start: 0.7825 (p0) cc_final: 0.7303 (t0) REVERT: L 47 ILE cc_start: 0.8685 (mm) cc_final: 0.8462 (mt) REVERT: L 202 LYS cc_start: 0.7443 (mmtt) cc_final: 0.7180 (mmmm) REVERT: M 20 MET cc_start: 0.8219 (mmm) cc_final: 0.7966 (mmp) REVERT: M 26 LEU cc_start: 0.7751 (mt) cc_final: 0.7526 (tp) REVERT: M 61 PHE cc_start: 0.7379 (t80) cc_final: 0.6265 (m-10) REVERT: M 86 LEU cc_start: 0.8676 (tp) cc_final: 0.8424 (mm) REVERT: UU 6 GLU cc_start: 0.4794 (OUTLIER) cc_final: 0.4366 (mt-10) REVERT: aa 3 LYS cc_start: 0.7752 (mttt) cc_final: 0.7324 (mttp) REVERT: ac 10 ILE cc_start: 0.8065 (mm) cc_final: 0.7833 (mt) REVERT: ac 30 MET cc_start: 0.8247 (ttt) cc_final: 0.7979 (ttm) REVERT: ad 9 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7593 (mpp) REVERT: ad 52 ASN cc_start: 0.7621 (m110) cc_final: 0.7183 (m110) REVERT: af 14 ARG cc_start: 0.6897 (mtp-110) cc_final: 0.6548 (mtm180) REVERT: af 30 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6853 (tpt) REVERT: ag 36 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8672 (mt) REVERT: ah 33 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7924 (tt) REVERT: ai 6 LYS cc_start: 0.7193 (mptp) cc_final: 0.6985 (mptp) REVERT: ai 9 MET cc_start: 0.6836 (mtp) cc_final: 0.6566 (mtm) REVERT: aj 20 GLN cc_start: 0.7592 (tt0) cc_final: 0.7316 (tt0) REVERT: aj 45 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: ak 11 PHE cc_start: 0.6611 (m-80) cc_final: 0.6373 (m-80) REVERT: am 14 ARG cc_start: 0.5040 (mtm180) cc_final: 0.4610 (mtm180) REVERT: an 40 SER cc_start: 0.4807 (p) cc_final: 0.4225 (t) REVERT: ba 15 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: bd 26 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7600 (t) REVERT: bf 36 ILE cc_start: 0.8207 (mt) cc_final: 0.7952 (tt) REVERT: bg 25 MET cc_start: 0.7129 (mmm) cc_final: 0.6711 (mmm) REVERT: bg 30 LEU cc_start: 0.8008 (tp) cc_final: 0.7732 (tp) REVERT: bh 29 TRP cc_start: 0.6796 (m100) cc_final: 0.6537 (m100) REVERT: bm 25 MET cc_start: 0.5914 (mmt) cc_final: 0.5626 (mmm) REVERT: bn 25 MET cc_start: 0.5244 (tpp) cc_final: 0.4928 (mmm) REVERT: bn 49 PHE cc_start: 0.5078 (OUTLIER) cc_final: 0.4828 (m-80) REVERT: h 52 ASN cc_start: 0.7836 (p0) cc_final: 0.7296 (t0) REVERT: h 163 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7458 (pttp) REVERT: l 47 ILE cc_start: 0.8698 (mm) cc_final: 0.8467 (mt) REVERT: l 202 LYS cc_start: 0.7436 (mmtt) cc_final: 0.7179 (mmmm) REVERT: m 20 MET cc_start: 0.8234 (mmm) cc_final: 0.7981 (mmp) REVERT: m 26 LEU cc_start: 0.7742 (mt) cc_final: 0.7513 (tp) REVERT: m 61 PHE cc_start: 0.7436 (t80) cc_final: 0.6298 (m-10) REVERT: m 86 LEU cc_start: 0.8672 (tp) cc_final: 0.8408 (mm) REVERT: uu 6 GLU cc_start: 0.4890 (OUTLIER) cc_final: 0.4512 (mt-10) REVERT: x 58 GLN cc_start: 0.6926 (mp10) cc_final: 0.6699 (mp10) outliers start: 90 outliers final: 50 residues processed: 697 average time/residue: 1.2917 time to fit residues: 1154.0263 Evaluate side-chains 686 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 619 time to evaluate : 4.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 5 TYR Chi-restraints excluded: chain AF residue 10 ILE Chi-restraints excluded: chain AF residue 14 ARG Chi-restraints excluded: chain AF residue 30 MET Chi-restraints excluded: chain AG residue 36 LEU Chi-restraints excluded: chain AI residue 10 ILE Chi-restraints excluded: chain AJ residue 33 LEU Chi-restraints excluded: chain AJ residue 37 SER Chi-restraints excluded: chain AJ residue 45 GLU Chi-restraints excluded: chain AK residue 47 SER Chi-restraints excluded: chain AL residue 2 SER Chi-restraints excluded: chain AM residue 34 ILE Chi-restraints excluded: chain BA residue 15 GLU Chi-restraints excluded: chain BA residue 26 SER Chi-restraints excluded: chain BD residue 26 SER Chi-restraints excluded: chain BD residue 30 LEU Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BE residue 14 ASP Chi-restraints excluded: chain BF residue 26 SER Chi-restraints excluded: chain BI residue 22 SER Chi-restraints excluded: chain BJ residue 44 ILE Chi-restraints excluded: chain BK residue 25 MET Chi-restraints excluded: chain BK residue 36 ILE Chi-restraints excluded: chain BL residue 40 LEU Chi-restraints excluded: chain BN residue 49 PHE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain UA residue 19 PHE Chi-restraints excluded: chain UA residue 22 MET Chi-restraints excluded: chain UU residue 6 GLU Chi-restraints excluded: chain ad residue 9 MET Chi-restraints excluded: chain ae residue 5 TYR Chi-restraints excluded: chain af residue 10 ILE Chi-restraints excluded: chain af residue 30 MET Chi-restraints excluded: chain ag residue 36 LEU Chi-restraints excluded: chain ah residue 33 LEU Chi-restraints excluded: chain ai residue 10 ILE Chi-restraints excluded: chain ai residue 37 SER Chi-restraints excluded: chain aj residue 37 SER Chi-restraints excluded: chain aj residue 45 GLU Chi-restraints excluded: chain ak residue 47 SER Chi-restraints excluded: chain am residue 34 ILE Chi-restraints excluded: chain ba residue 15 GLU Chi-restraints excluded: chain ba residue 26 SER Chi-restraints excluded: chain bd residue 26 SER Chi-restraints excluded: chain bd residue 40 LEU Chi-restraints excluded: chain be residue 14 ASP Chi-restraints excluded: chain bf residue 26 SER Chi-restraints excluded: chain bi residue 22 SER Chi-restraints excluded: chain bj residue 44 ILE Chi-restraints excluded: chain bk residue 36 ILE Chi-restraints excluded: chain bl residue 40 LEU Chi-restraints excluded: chain bn residue 49 PHE Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 163 LYS Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain ua residue 19 PHE Chi-restraints excluded: chain ua residue 22 MET Chi-restraints excluded: chain uu residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 10.0000 chunk 419 optimal weight: 0.9990 chunk 256 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 291 optimal weight: 0.6980 chunk 440 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 chunk 350 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 270 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 20 GLN AE 20 GLN ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS M 188 ASN ae 20 GLN ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** al 20 GLN bd 16 GLN bg 21 HIS m 188 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 47562 Z= 0.180 Angle : 2.311 26.985 65208 Z= 0.784 Chirality : 0.037 0.171 6386 Planarity : 0.004 0.043 7950 Dihedral : 18.917 179.991 8630 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.05 % Allowed : 14.59 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.12), residues: 4532 helix: 2.61 (0.09), residues: 3002 sheet: 2.09 (1.04), residues: 22 loop : 0.11 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRPBJ 29 HIS 0.013 0.001 HISbl 21 PHE 0.020 0.001 PHEAN 25 TYR 0.026 0.001 TYRae 5 ARG 0.003 0.000 ARGal 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9064 Ramachandran restraints generated. 4532 Oldfield, 0 Emsley, 4532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 647 time to evaluate : 3.715 Fit side-chains revert: symmetry clash REVERT: AA 3 LYS cc_start: 0.7571 (mttt) cc_final: 0.7111 (mttp) REVERT: AC 30 MET cc_start: 0.8365 (ttt) cc_final: 0.8090 (ttm) REVERT: AD 52 ASN cc_start: 0.7649 (m110) cc_final: 0.7199 (m110) REVERT: AF 30 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7228 (tpt) REVERT: AH 33 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7930 (tt) REVERT: AI 9 MET cc_start: 0.6876 (mtp) cc_final: 0.6659 (mtp) REVERT: AJ 45 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6613 (mp0) REVERT: AM 9 MET cc_start: 0.4494 (mmm) cc_final: 0.3630 (ptt) REVERT: AM 14 ARG cc_start: 0.4999 (mtm180) cc_final: 0.4616 (mtm180) REVERT: BA 15 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: BD 30 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8247 (tm) REVERT: BE 15 GLU cc_start: 0.6476 (mm-30) cc_final: 0.5875 (mt-10) REVERT: BF 36 ILE cc_start: 0.8206 (mt) cc_final: 0.7948 (tt) REVERT: BG 25 MET cc_start: 0.7141 (mmm) cc_final: 0.6713 (mmm) REVERT: BG 30 LEU cc_start: 0.7996 (tp) cc_final: 0.7739 (tp) REVERT: BH 29 TRP cc_start: 0.6790 (m100) cc_final: 0.6537 (m100) REVERT: BM 25 MET cc_start: 0.5792 (mmt) cc_final: 0.5477 (mmm) REVERT: BN 25 MET cc_start: 0.4840 (tpp) cc_final: 0.4552 (mmm) REVERT: BN 49 PHE cc_start: 0.5074 (OUTLIER) cc_final: 0.4852 (m-80) REVERT: H 52 ASN cc_start: 0.7843 (p0) cc_final: 0.7297 (t0) REVERT: H 154 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7461 (ttp-170) REVERT: L 91 ILE cc_start: 0.8888 (mt) cc_final: 0.8678 (mt) REVERT: L 202 LYS cc_start: 0.7473 (mmtt) cc_final: 0.7198 (mmmm) REVERT: M 20 MET cc_start: 0.8236 (mmm) cc_final: 0.7976 (mmp) REVERT: M 26 LEU cc_start: 0.7745 (mt) cc_final: 0.7497 (tp) REVERT: M 61 PHE cc_start: 0.7371 (t80) cc_final: 0.6235 (m-10) REVERT: M 86 LEU cc_start: 0.8684 (tp) cc_final: 0.8428 (mm) REVERT: UU 6 GLU cc_start: 0.4828 (OUTLIER) cc_final: 0.4416 (mt-10) REVERT: UU 23 ILE cc_start: 0.7643 (mt) cc_final: 0.7396 (mm) REVERT: aa 3 LYS cc_start: 0.7701 (mttt) cc_final: 0.7348 (mtmm) REVERT: ac 10 ILE cc_start: 0.8067 (mm) cc_final: 0.7833 (mt) REVERT: ac 30 MET cc_start: 0.8239 (ttt) cc_final: 0.7973 (ttm) REVERT: ad 52 ASN cc_start: 0.7639 (m110) cc_final: 0.7177 (m110) REVERT: af 14 ARG cc_start: 0.6821 (mtp-110) cc_final: 0.6486 (mtm180) REVERT: af 30 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.6876 (tpt) REVERT: ah 33 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7937 (tt) REVERT: ai 9 MET cc_start: 0.6794 (mtp) cc_final: 0.6351 (mtt) REVERT: aj 20 GLN cc_start: 0.7574 (tt0) cc_final: 0.7353 (tt0) REVERT: aj 45 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6618 (mp0) REVERT: ak 11 PHE cc_start: 0.6673 (m-80) cc_final: 0.6404 (m-80) REVERT: am 9 MET cc_start: 0.4558 (mmm) cc_final: 0.3758 (ttp) REVERT: am 14 ARG cc_start: 0.5029 (mtm180) cc_final: 0.4613 (mtm180) REVERT: bd 26 SER cc_start: 0.7878 (OUTLIER) cc_final: 0.7577 (t) REVERT: be 15 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5895 (mt-10) REVERT: bf 36 ILE cc_start: 0.8215 (mt) cc_final: 0.7964 (tt) REVERT: bg 25 MET cc_start: 0.7015 (mmm) cc_final: 0.6551 (mmm) REVERT: bg 30 LEU cc_start: 0.7994 (tp) cc_final: 0.7738 (tp) REVERT: bh 29 TRP cc_start: 0.6766 (m100) cc_final: 0.6546 (m100) REVERT: bm 25 MET cc_start: 0.5890 (mmt) cc_final: 0.5586 (mmm) REVERT: bn 25 MET cc_start: 0.5152 (tpp) cc_final: 0.4900 (mmm) REVERT: bn 49 PHE cc_start: 0.5081 (OUTLIER) cc_final: 0.4847 (m-80) REVERT: h 52 ASN cc_start: 0.7829 (p0) cc_final: 0.7288 (t0) REVERT: h 163 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7474 (pttp) REVERT: l 202 LYS cc_start: 0.7444 (mmtt) cc_final: 0.7173 (mmmm) REVERT: m 20 MET cc_start: 0.8248 (mmm) cc_final: 0.7983 (mmp) REVERT: m 26 LEU cc_start: 0.7740 (mt) cc_final: 0.7489 (tp) REVERT: m 61 PHE cc_start: 0.7423 (t80) cc_final: 0.6270 (m-10) REVERT: m 86 LEU cc_start: 0.8679 (tp) cc_final: 0.8415 (mm) REVERT: uu 6 GLU cc_start: 0.4907 (OUTLIER) cc_final: 0.4545 (mt-10) REVERT: uu 23 ILE cc_start: 0.7617 (mt) cc_final: 0.7370 (mm) REVERT: x 58 GLN cc_start: 0.6952 (mp10) cc_final: 0.6644 (mp10) outliers start: 79 outliers final: 49 residues processed: 696 average time/residue: 1.2992 time to fit residues: 1156.9759 Evaluate side-chains 685 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 622 time to evaluate : 4.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 5 TYR Chi-restraints excluded: chain AF residue 10 ILE Chi-restraints excluded: chain AF residue 14 ARG Chi-restraints excluded: chain AF residue 30 MET Chi-restraints excluded: chain AH residue 33 LEU Chi-restraints excluded: chain AI residue 10 ILE Chi-restraints excluded: chain AI residue 37 SER Chi-restraints excluded: chain AJ residue 33 LEU Chi-restraints excluded: chain AJ residue 37 SER Chi-restraints excluded: chain AJ residue 45 GLU Chi-restraints excluded: chain AK residue 47 SER Chi-restraints excluded: chain AL residue 2 SER Chi-restraints excluded: chain BA residue 15 GLU Chi-restraints excluded: chain BA residue 26 SER Chi-restraints excluded: chain BD residue 26 SER Chi-restraints excluded: chain BD residue 30 LEU Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BE residue 14 ASP Chi-restraints excluded: chain BF residue 26 SER Chi-restraints excluded: chain BI residue 22 SER Chi-restraints excluded: chain BJ residue 44 ILE Chi-restraints excluded: chain BK residue 36 ILE Chi-restraints excluded: chain BL residue 40 LEU Chi-restraints excluded: chain BN residue 49 PHE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 247 CYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain UA residue 19 PHE Chi-restraints excluded: chain UA residue 22 MET Chi-restraints excluded: chain UU residue 6 GLU Chi-restraints excluded: chain ae residue 5 TYR Chi-restraints excluded: chain af residue 10 ILE Chi-restraints excluded: chain af residue 30 MET Chi-restraints excluded: chain ah residue 33 LEU Chi-restraints excluded: chain ai residue 10 ILE Chi-restraints excluded: chain aj residue 37 SER Chi-restraints excluded: chain aj residue 45 GLU Chi-restraints excluded: chain ak residue 47 SER Chi-restraints excluded: chain al residue 2 SER Chi-restraints excluded: chain an residue 30 MET Chi-restraints excluded: chain ba residue 15 GLU Chi-restraints excluded: chain ba residue 26 SER Chi-restraints excluded: chain bd residue 26 SER Chi-restraints excluded: chain bd residue 40 LEU Chi-restraints excluded: chain be residue 14 ASP Chi-restraints excluded: chain bf residue 26 SER Chi-restraints excluded: chain bj residue 44 ILE Chi-restraints excluded: chain bk residue 36 ILE Chi-restraints excluded: chain bl residue 40 LEU Chi-restraints excluded: chain bn residue 49 PHE Chi-restraints excluded: chain h residue 72 THR Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 163 LYS Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 247 CYS Chi-restraints excluded: chain m residue 62 SER Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain ua residue 19 PHE Chi-restraints excluded: chain ua residue 22 MET Chi-restraints excluded: chain uu residue 6 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 5.9990 chunk 373 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 351 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 360 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 20 GLN ** AC 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 20 GLN ** AI 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 20 GLN ** AL 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 16 GLN BG 21 HIS M 188 ASN X 18 ASN X 60 ASN ab 20 GLN ae 20 GLN ** ai 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** bd 16 GLN bg 21 HIS m 188 ASN x 18 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.152440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.111753 restraints weight = 49563.926| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.85 r_work: 0.2829 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 47562 Z= 0.297 Angle : 2.358 26.401 65208 Z= 0.806 Chirality : 0.042 0.203 6386 Planarity : 0.005 0.043 7950 Dihedral : 19.371 179.987 8630 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.18 % Allowed : 14.56 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.12), residues: 4532 helix: 2.19 (0.09), residues: 3032 sheet: 0.78 (0.72), residues: 42 loop : -0.01 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRPAH 8 HIS 0.014 0.002 HISbl 21 PHE 0.028 0.002 PHEAN 25 TYR 0.024 0.002 TYRae 5 ARG 0.004 0.000 ARGAE 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18469.43 seconds wall clock time: 326 minutes 7.32 seconds (19567.32 seconds total)